1<?xml version="1.0" encoding="UTF-8"?> 2<ui version="4.0"> 3 <class>Primer3Dialog</class> 4 <widget class="QDialog" name="Primer3Dialog"> 5 <property name="geometry"> 6 <rect> 7 <x>0</x> 8 <y>0</y> 9 <width>1085</width> 10 <height>628</height> 11 </rect> 12 </property> 13 <property name="sizePolicy"> 14 <sizepolicy hsizetype="Preferred" vsizetype="Preferred"> 15 <horstretch>0</horstretch> 16 <verstretch>0</verstretch> 17 </sizepolicy> 18 </property> 19 <property name="windowTitle"> 20 <string>Primer Designer</string> 21 </property> 22 <layout class="QVBoxLayout" name="verticalLayout"> 23 <item> 24 <widget class="QTabWidget" name="tabWidget"> 25 <property name="enabled"> 26 <bool>true</bool> 27 </property> 28 <property name="currentIndex"> 29 <number>0</number> 30 </property> 31 <widget class="QWidget" name="tab_Main"> 32 <attribute name="title"> 33 <string>Main</string> 34 </attribute> 35 <layout class="QVBoxLayout" name="verticalLayout_4"> 36 <item> 37 <layout class="QGridLayout" name="gridLayout_2"> 38 <item row="0" column="0"> 39 <widget class="QLabel" name="label_EXCLUDED_REGION"> 40 <property name="text"> 41 <string>Excluded regions</string> 42 </property> 43 </widget> 44 </item> 45 <item row="1" column="0"> 46 <widget class="QLabel" name="label_TARGET"> 47 <property name="text"> 48 <string>Targets</string> 49 </property> 50 </widget> 51 </item> 52 <item row="0" column="1"> 53 <widget class="QLineEdit" name="edit_EXCLUDED_REGION"> 54 <property name="toolTip"> 55 <string><html><head/><body><p>Primer oligos may not overlap any region specified in this tag. The associated value must be a space-separated list of</p><p><span style=" font-weight:600;">start,length</span></p><p>pairs where start is the index of the first base of the excluded region, and length is its length. This tag is useful for tasks such as excluding regions of low sequence quality or for excluding regions containing repetitive elements such as ALUs or LINEs.</p></body></html></string> 56 </property> 57 </widget> 58 </item> 59 <item row="1" column="1"> 60 <widget class="QLineEdit" name="edit_TARGET"> 61 <property name="toolTip"> 62 <string><html><head/><body><p>If one or more Targets is specified then a legal primer pair must flank at least one of them. A Target might be a simple sequence repeat site (for example a CA repeat) or a single-base-pair polymorphism. The value should be a space-separated list of </p><p><span style=" font-weight:600;">start,length</span></p><p>pairs where start is the index of the first base of a Target, and length is its length.</p></body></html></string> 63 </property> 64 </widget> 65 </item> 66 <item row="1" column="2"> 67 <spacer name="horizontalSpacer_5"> 68 <property name="orientation"> 69 <enum>Qt::Horizontal</enum> 70 </property> 71 <property name="sizeHint" stdset="0"> 72 <size> 73 <width>40</width> 74 <height>20</height> 75 </size> 76 </property> 77 </spacer> 78 </item> 79 <item row="0" column="2"> 80 <spacer name="horizontalSpacer_7"> 81 <property name="orientation"> 82 <enum>Qt::Horizontal</enum> 83 </property> 84 <property name="sizeHint" stdset="0"> 85 <size> 86 <width>40</width> 87 <height>20</height> 88 </size> 89 </property> 90 </spacer> 91 </item> 92 </layout> 93 </item> 94 <item> 95 <widget class="Line" name="line"> 96 <property name="orientation"> 97 <enum>Qt::Horizontal</enum> 98 </property> 99 </widget> 100 </item> 101 <item> 102 <layout class="QGridLayout" name="gridLayout_7"> 103 <item row="0" column="0"> 104 <widget class="QLabel" name="label_PRIMER_PRODUCT_SIZE_RANGE"> 105 <property name="text"> 106 <string>Product size ranges</string> 107 </property> 108 </widget> 109 </item> 110 <item row="0" column="1"> 111 <widget class="QLineEdit" name="edit_PRIMER_PRODUCT_SIZE_RANGE"> 112 <property name="toolTip"> 113 <string><html><head/><body><p>A list of product size ranges, for example:</p><p><span style="font-weight:600;"> 150-250 100-300 301-400 </span></p><p>Primer3 first tries to pick primers in the first range. If that is not possible, it goes to the next range and tries again. It continues in this way until it has either picked all necessary primers or until there are no more ranges. For technical reasons this option makes much lighter computational demands than the Product Size option.</p></body></html></string> 114 </property> 115 </widget> 116 </item> 117 <item row="0" column="2"> 118 <widget class="QLabel" name="label_PRIMER_MISPRIMING_LIBRARY"> 119 <property name="text"> 120 <string>Mispriming/Repeat library</string> 121 </property> 122 </widget> 123 </item> 124 <item row="0" column="3"> 125 <widget class="QComboBox" name="combobox_PRIMER_MISPRIMING_LIBRARY"> 126 <property name="enabled"> 127 <bool>true</bool> 128 </property> 129 <property name="toolTip"> 130 <string><html><head/><body><p>This selection indicates what mispriming library (if any) Primer3 should use to screen for interspersed repeats or for other sequence to avoid as a location for primers.</p></body></html></string> 131 </property> 132 </widget> 133 </item> 134 </layout> 135 </item> 136 <item> 137 <widget class="Line" name="line_3"> 138 <property name="orientation"> 139 <enum>Qt::Horizontal</enum> 140 </property> 141 </widget> 142 </item> 143 <item> 144 <layout class="QGridLayout" name="gridLayout_8"> 145 <item row="1" column="0"> 146 <widget class="QLabel" name="label_PRIMER_NUM_RETURN"> 147 <property name="text"> 148 <string>Number to return</string> 149 </property> 150 </widget> 151 </item> 152 <item row="2" column="0"> 153 <widget class="QLabel" name="label_PRIMER_MAX_MISPRIMING"> 154 <property name="text"> 155 <string>Max repeat mispriming</string> 156 </property> 157 </widget> 158 </item> 159 <item row="3" column="0"> 160 <widget class="QLabel" name="label_PRIMER_MAX_TEMPLATE_MISPRIMING"> 161 <property name="text"> 162 <string>Max template mispriming</string> 163 </property> 164 </widget> 165 </item> 166 <item row="1" column="2"> 167 <widget class="QLabel" name="label_PRIMER_MAX_END_STABILITY"> 168 <property name="text"> 169 <string>Max 3' stability</string> 170 </property> 171 </widget> 172 </item> 173 <item row="2" column="2"> 174 <widget class="QLabel" name="label_PRIMER_PAIR_MAX_MISPRIMING"> 175 <property name="text"> 176 <string>Pair max repeat mispriming</string> 177 </property> 178 </widget> 179 </item> 180 <item row="3" column="2"> 181 <widget class="QLabel" name="label_PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING"> 182 <property name="text"> 183 <string>Pair max template mispriming</string> 184 </property> 185 </widget> 186 </item> 187 <item row="1" column="4"> 188 <spacer name="horizontalSpacer_8"> 189 <property name="orientation"> 190 <enum>Qt::Horizontal</enum> 191 </property> 192 <property name="sizeHint" stdset="0"> 193 <size> 194 <width>40</width> 195 <height>20</height> 196 </size> 197 </property> 198 </spacer> 199 </item> 200 <item row="2" column="4"> 201 <spacer name="horizontalSpacer_4"> 202 <property name="orientation"> 203 <enum>Qt::Horizontal</enum> 204 </property> 205 <property name="sizeHint" stdset="0"> 206 <size> 207 <width>40</width> 208 <height>20</height> 209 </size> 210 </property> 211 </spacer> 212 </item> 213 <item row="3" column="4"> 214 <spacer name="horizontalSpacer_30"> 215 <property name="orientation"> 216 <enum>Qt::Horizontal</enum> 217 </property> 218 <property name="sizeHint" stdset="0"> 219 <size> 220 <width>40</width> 221 <height>20</height> 222 </size> 223 </property> 224 </spacer> 225 </item> 226 <item row="1" column="1"> 227 <widget class="QSpinBox" name="edit_PRIMER_NUM_RETURN"> 228 <property name="sizePolicy"> 229 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 230 <horstretch>0</horstretch> 231 <verstretch>0</verstretch> 232 </sizepolicy> 233 </property> 234 <property name="toolTip"> 235 <string><html><head/><body><p>The maximum number of primer pairs to return.</p><p>Primer pairs returned are sorted by their &quot;quality&quot;, in other words by the value of the objective function (where a lower number indicates a better primer pair).</p><p>Caution: setting this parameter to a large value will increase running time.</p></body></html></string> 236 </property> 237 <property name="minimum"> 238 <number>1</number> 239 </property> 240 <property name="maximum"> 241 <number>9999</number> 242 </property> 243 </widget> 244 </item> 245 <item row="1" column="3"> 246 <widget class="QDoubleSpinBox" name="edit_PRIMER_MAX_END_STABILITY"> 247 <property name="sizePolicy"> 248 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 249 <horstretch>0</horstretch> 250 <verstretch>0</verstretch> 251 </sizepolicy> 252 </property> 253 <property name="toolTip"> 254 <string><html><head/><body><p>The maximum stability for the last five 3' bases of a left or right primer.</p><p>Bigger numbers mean more stable 3' ends. The value is the maximum delta G (kcal/mol) for duplex disruption for the five 3' bases as calculated using the Nearest-Neighbor parameter values specified by the option of 'Table of thermodynamic parameters'.</p></body></html></string> 255 </property> 256 <property name="maximum"> 257 <double>9999.989999999999782</double> 258 </property> 259 </widget> 260 </item> 261 <item row="2" column="1"> 262 <widget class="QDoubleSpinBox" name="edit_PRIMER_MAX_MISPRIMING"> 263 <property name="sizePolicy"> 264 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 265 <horstretch>0</horstretch> 266 <verstretch>0</verstretch> 267 </sizepolicy> 268 </property> 269 <property name="toolTip"> 270 <string><html><head/><body><p>The maximum allowed weighted similarity with any sequence in Mispriming Library.</p></body></html></string> 271 </property> 272 <property name="maximum"> 273 <double>9999.989999999999782</double> 274 </property> 275 </widget> 276 </item> 277 <item row="2" column="3"> 278 <widget class="QDoubleSpinBox" name="edit_PRIMER_PAIR_MAX_MISPRIMING"> 279 <property name="sizePolicy"> 280 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 281 <horstretch>0</horstretch> 282 <verstretch>0</verstretch> 283 </sizepolicy> 284 </property> 285 <property name="toolTip"> 286 <string><html><head/><body><p>The maximum allowed sum of similarities of a primer pair (one similarity for each primer) with any single sequence in Mispriming Library. </p><p>Library sequence weights are not used in computing the sum of similarities.</p></body></html></string> 287 </property> 288 <property name="maximum"> 289 <double>9999.989999999999782</double> 290 </property> 291 </widget> 292 </item> 293 <item row="3" column="1"> 294 <widget class="QDoubleSpinBox" name="edit_PRIMER_MAX_TEMPLATE_MISPRIMING"> 295 <property name="sizePolicy"> 296 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 297 <horstretch>0</horstretch> 298 <verstretch>0</verstretch> 299 </sizepolicy> 300 </property> 301 <property name="toolTip"> 302 <string><html><head/><body><p>The maximum allowed similarity to ectopic sites in the sequence from which you are designing the primers.</p><p>The scoring system is the same as used for Max Mispriming, except that an ambiguity code is never treated as a consensus.</p></body></html></string> 303 </property> 304 <property name="maximum"> 305 <double>9999.989999999999782</double> 306 </property> 307 </widget> 308 </item> 309 <item row="3" column="3"> 310 <widget class="QDoubleSpinBox" name="edit_PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING"> 311 <property name="sizePolicy"> 312 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 313 <horstretch>0</horstretch> 314 <verstretch>0</verstretch> 315 </sizepolicy> 316 </property> 317 <property name="toolTip"> 318 <string><html><head/><body><p>The maximum allowed summed similarity of both primers to ectopic sites in the sequence from which you are designing the primers.</p><p>The scoring system is the same as used for Max Mispriming, except that an ambiguity code is never treated as a consensus.</p></body></html></string> 319 </property> 320 <property name="maximum"> 321 <double>9999.989999999999782</double> 322 </property> 323 </widget> 324 </item> 325 <item row="5" column="0"> 326 <widget class="QLabel" name="label_PRIMER_START_CODON_POSITION"> 327 <property name="text"> 328 <string>Start codon position</string> 329 </property> 330 </widget> 331 </item> 332 <item row="5" column="1"> 333 <widget class="QLineEdit" name="edit_PRIMER_START_CODON_POSITION"> 334 <property name="toolTip"> 335 <string><html><head/><body><p>Index of the first base of a start codon.</p><p>This parameter allows Primer3 to select primer pairs to create in-frame amplicons e.g. to create a template for a fusion protein. Primer3 will attempt to select an in-frame left primer, ideally starting at or to the left of the start codon, or to the right if necessary. Negative values of this parameter are legal if the actual start codon is to the left of available sequence. If this parameter is non-negative Primer3 signals an error if the codon at the position specified by this parameter is not an ATG. A value less than or equal to -10^6 indicates that Primer3 should ignore this parameter. Primer3 selects the position of the right primer by scanning right from the left primer for a stop codon. Ideally the right primer will end at or after the stop codon.</p><p>This parameter should be considered EXPERIMENTAL. Please check the output carefully; some erroneous inputs might cause an error in Primer3.</p></body></html></string> 336 </property> 337 </widget> 338 </item> 339 <item row="5" column="2"> 340 <spacer name="horizontalSpacer_29"> 341 <property name="orientation"> 342 <enum>Qt::Horizontal</enum> 343 </property> 344 <property name="sizeHint" stdset="0"> 345 <size> 346 <width>40</width> 347 <height>20</height> 348 </size> 349 </property> 350 </spacer> 351 </item> 352 <item row="5" column="3"> 353 <spacer name="horizontalSpacer_28"> 354 <property name="orientation"> 355 <enum>Qt::Horizontal</enum> 356 </property> 357 <property name="sizeHint" stdset="0"> 358 <size> 359 <width>40</width> 360 <height>20</height> 361 </size> 362 </property> 363 </spacer> 364 </item> 365 <item row="5" column="4"> 366 <spacer name="horizontalSpacer_33"> 367 <property name="orientation"> 368 <enum>Qt::Horizontal</enum> 369 </property> 370 <property name="sizeHint" stdset="0"> 371 <size> 372 <width>40</width> 373 <height>20</height> 374 </size> 375 </property> 376 </spacer> 377 </item> 378 </layout> 379 </item> 380 <item> 381 <widget class="Line" name="line_5"> 382 <property name="orientation"> 383 <enum>Qt::Horizontal</enum> 384 </property> 385 </widget> 386 </item> 387 <item> 388 <layout class="QGridLayout" name="gridLayout_3"> 389 <item row="0" column="0"> 390 <widget class="QCheckBox" name="checkbox_PICK_LEFT"> 391 <property name="enabled"> 392 <bool>true</bool> 393 </property> 394 <property name="text"> 395 <string>Pick left primer</string> 396 </property> 397 <property name="checked"> 398 <bool>true</bool> 399 </property> 400 <property name="tristate"> 401 <bool>false</bool> 402 </property> 403 </widget> 404 </item> 405 <item row="1" column="0"> 406 <widget class="QLabel" name="label_34"> 407 <property name="text"> 408 <string>or use left primer below</string> 409 </property> 410 </widget> 411 </item> 412 <item row="2" column="0"> 413 <widget class="QLineEdit" name="edit_PRIMER_LEFT_INPUT"> 414 <property name="enabled"> 415 <bool>true</bool> 416 </property> 417 </widget> 418 </item> 419 <item row="0" column="1"> 420 <widget class="QCheckBox" name="checkbox_PICK_HYBRO"> 421 <property name="enabled"> 422 <bool>true</bool> 423 </property> 424 <property name="text"> 425 <string>Pick hybridization probe (internal oligo)</string> 426 </property> 427 <property name="checkable"> 428 <bool>true</bool> 429 </property> 430 <property name="checked"> 431 <bool>false</bool> 432 </property> 433 </widget> 434 </item> 435 <item row="1" column="1"> 436 <widget class="QLabel" name="label_35"> 437 <property name="text"> 438 <string>or use oligo below</string> 439 </property> 440 </widget> 441 </item> 442 <item row="2" column="1"> 443 <widget class="QLineEdit" name="edit_PRIMER_INTERNAL_OLIGO_INPUT"> 444 <property name="enabled"> 445 <bool>false</bool> 446 </property> 447 </widget> 448 </item> 449 <item row="0" column="2"> 450 <widget class="QCheckBox" name="checkbox_PICK_RIGHT"> 451 <property name="enabled"> 452 <bool>true</bool> 453 </property> 454 <property name="acceptDrops"> 455 <bool>false</bool> 456 </property> 457 <property name="text"> 458 <string>Pick right primer</string> 459 </property> 460 <property name="checked"> 461 <bool>true</bool> 462 </property> 463 <property name="tristate"> 464 <bool>false</bool> 465 </property> 466 </widget> 467 </item> 468 <item row="1" column="2"> 469 <widget class="QLabel" name="label_36"> 470 <property name="text"> 471 <string>or use right primer below (5' to 3' on opposite strand)</string> 472 </property> 473 </widget> 474 </item> 475 <item row="2" column="2"> 476 <widget class="QLineEdit" name="edit_PRIMER_RIGHT_INPUT"> 477 <property name="enabled"> 478 <bool>true</bool> 479 </property> 480 </widget> 481 </item> 482 </layout> 483 </item> 484 <item> 485 <spacer name="verticalSpacer"> 486 <property name="orientation"> 487 <enum>Qt::Vertical</enum> 488 </property> 489 <property name="sizeHint" stdset="0"> 490 <size> 491 <width>20</width> 492 <height>40</height> 493 </size> 494 </property> 495 </spacer> 496 </item> 497 </layout> 498 </widget> 499 <widget class="QWidget" name="tab_General_Settings"> 500 <attribute name="title"> 501 <string>General Settings</string> 502 </attribute> 503 <attribute name="toolTip"> 504 <string><html><head/><body><p>This section covers such settings as primer size, temperature, GC and other general settings.</p></body></html></string> 505 </attribute> 506 <layout class="QVBoxLayout" name="verticalLayout_13"> 507 <item> 508 <layout class="QGridLayout" name="gridLayout"> 509 <item row="0" column="0"> 510 <widget class="QLabel" name="label_PRIMER_SIZE"> 511 <property name="text"> 512 <string>Primer size</string> 513 </property> 514 </widget> 515 </item> 516 <item row="0" column="2"> 517 <widget class="QLabel" name="label_PRIMER_MIN_SIZE"> 518 <property name="text"> 519 <string>Min</string> 520 </property> 521 </widget> 522 </item> 523 <item row="0" column="4"> 524 <widget class="QLabel" name="label_PRIMER_OPT_SIZE"> 525 <property name="text"> 526 <string>Opt</string> 527 </property> 528 </widget> 529 </item> 530 <item row="0" column="6"> 531 <widget class="QLabel" name="label_PRIMER_MAX_SIZE"> 532 <property name="text"> 533 <string>Max</string> 534 </property> 535 </widget> 536 </item> 537 <item row="1" column="0"> 538 <widget class="QLabel" name="label_PRIMER_TM"> 539 <property name="text"> 540 <string>Primer Tm</string> 541 </property> 542 </widget> 543 </item> 544 <item row="1" column="2"> 545 <widget class="QLabel" name="label_PRIMER_MIN_TM"> 546 <property name="text"> 547 <string>Min</string> 548 </property> 549 </widget> 550 </item> 551 <item row="1" column="4"> 552 <widget class="QLabel" name="label_PRIMER_OPT_TM"> 553 <property name="text"> 554 <string>Opt</string> 555 </property> 556 </widget> 557 </item> 558 <item row="1" column="6"> 559 <widget class="QLabel" name="label_PRIMER_MAX_TM"> 560 <property name="text"> 561 <string>Max</string> 562 </property> 563 </widget> 564 </item> 565 <item row="2" column="0"> 566 <widget class="QLabel" name="label_PRIMER_PRODUCT_TM"> 567 <property name="text"> 568 <string>Product Tm</string> 569 </property> 570 </widget> 571 </item> 572 <item row="2" column="2"> 573 <widget class="QLabel" name="label_PRIMER_PRODUCT_MIN_TM"> 574 <property name="text"> 575 <string>Min</string> 576 </property> 577 </widget> 578 </item> 579 <item row="2" column="4"> 580 <widget class="QLabel" name="label_PRIMER_PRODUCT_OPT_TM"> 581 <property name="text"> 582 <string>Opt</string> 583 </property> 584 </widget> 585 </item> 586 <item row="2" column="6"> 587 <widget class="QLabel" name="label_PRIMER_PRODUCT_MAX_TM"> 588 <property name="text"> 589 <string>Max</string> 590 </property> 591 </widget> 592 </item> 593 <item row="3" column="0"> 594 <widget class="QLabel" name="label_PRIMER_GC_PERCENT"> 595 <property name="text"> 596 <string>Primer GC%</string> 597 </property> 598 </widget> 599 </item> 600 <item row="3" column="2"> 601 <widget class="QLabel" name="label_PRIMER_MIN_GC_PERCENT"> 602 <property name="text"> 603 <string>Min</string> 604 </property> 605 </widget> 606 </item> 607 <item row="3" column="4"> 608 <widget class="QLabel" name="label_PRIMER_OPT_GC_PERCENT"> 609 <property name="text"> 610 <string>Opt</string> 611 </property> 612 </widget> 613 </item> 614 <item row="3" column="6"> 615 <widget class="QLabel" name="label_PRIMER_MAX_GC_PERCENT"> 616 <property name="text"> 617 <string>Max</string> 618 </property> 619 </widget> 620 </item> 621 <item row="0" column="8"> 622 <spacer name="horizontalSpacer_6"> 623 <property name="orientation"> 624 <enum>Qt::Horizontal</enum> 625 </property> 626 <property name="sizeHint" stdset="0"> 627 <size> 628 <width>40</width> 629 <height>20</height> 630 </size> 631 </property> 632 </spacer> 633 </item> 634 <item row="3" column="8"> 635 <spacer name="horizontalSpacer_12"> 636 <property name="orientation"> 637 <enum>Qt::Horizontal</enum> 638 </property> 639 <property name="sizeHint" stdset="0"> 640 <size> 641 <width>40</width> 642 <height>20</height> 643 </size> 644 </property> 645 </spacer> 646 </item> 647 <item row="3" column="9"> 648 <spacer name="horizontalSpacer_18"> 649 <property name="orientation"> 650 <enum>Qt::Horizontal</enum> 651 </property> 652 <property name="sizeHint" stdset="0"> 653 <size> 654 <width>40</width> 655 <height>20</height> 656 </size> 657 </property> 658 </spacer> 659 </item> 660 <item row="0" column="9"> 661 <spacer name="horizontalSpacer_16"> 662 <property name="orientation"> 663 <enum>Qt::Horizontal</enum> 664 </property> 665 <property name="sizeHint" stdset="0"> 666 <size> 667 <width>40</width> 668 <height>20</height> 669 </size> 670 </property> 671 </spacer> 672 </item> 673 <item row="3" column="1"> 674 <spacer name="horizontalSpacer_31"> 675 <property name="orientation"> 676 <enum>Qt::Horizontal</enum> 677 </property> 678 <property name="sizeHint" stdset="0"> 679 <size> 680 <width>13</width> 681 <height>17</height> 682 </size> 683 </property> 684 </spacer> 685 </item> 686 <item row="2" column="1"> 687 <spacer name="horizontalSpacer_3"> 688 <property name="orientation"> 689 <enum>Qt::Horizontal</enum> 690 </property> 691 <property name="sizeHint" stdset="0"> 692 <size> 693 <width>13</width> 694 <height>17</height> 695 </size> 696 </property> 697 </spacer> 698 </item> 699 <item row="1" column="1"> 700 <spacer name="horizontalSpacer_2"> 701 <property name="orientation"> 702 <enum>Qt::Horizontal</enum> 703 </property> 704 <property name="sizeHint" stdset="0"> 705 <size> 706 <width>13</width> 707 <height>17</height> 708 </size> 709 </property> 710 </spacer> 711 </item> 712 <item row="0" column="1"> 713 <spacer name="horizontalSpacer_10"> 714 <property name="orientation"> 715 <enum>Qt::Horizontal</enum> 716 </property> 717 <property name="sizeHint" stdset="0"> 718 <size> 719 <width>13</width> 720 <height>17</height> 721 </size> 722 </property> 723 </spacer> 724 </item> 725 <item row="0" column="5"> 726 <widget class="QSpinBox" name="edit_PRIMER_OPT_SIZE"> 727 <property name="sizePolicy"> 728 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 729 <horstretch>0</horstretch> 730 <verstretch>0</verstretch> 731 </sizepolicy> 732 </property> 733 <property name="toolTip"> 734 <string><html><head/><body><p>Minimum, Optimum, and Maximum lengths (in bases) of a primer oligo.</p><p>Primer3 will not pick primers shorter than Min or longer than Max, and with default arguments will attempt to pick primers close with size close to Opt.</p><p>Min cannot be smaller than 1. Max cannot be larger than 36. (This limit is governed by maximum oligo size for which melting-temperature calculations are valid.)</p><p>Min cannot be greater than Max.</p></body></html></string> 735 </property> 736 </widget> 737 </item> 738 <item row="0" column="3"> 739 <widget class="QSpinBox" name="edit_PRIMER_MIN_SIZE"> 740 <property name="sizePolicy"> 741 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 742 <horstretch>0</horstretch> 743 <verstretch>0</verstretch> 744 </sizepolicy> 745 </property> 746 <property name="toolTip"> 747 <string><html><head/><body><p>Minimum, Optimum, and Maximum lengths (in bases) of a primer oligo.</p><p>Primer3 will not pick primers shorter than Min or longer than Max, and with default arguments will attempt to pick primers close with size close to Opt.</p><p>Min cannot be smaller than 1. Max cannot be larger than 36. (This limit is governed by maximum oligo size for which melting-temperature calculations are valid.)</p><p>Min cannot be greater than Max.</p></body></html></string> 748 </property> 749 </widget> 750 </item> 751 <item row="0" column="7"> 752 <widget class="QSpinBox" name="edit_PRIMER_MAX_SIZE"> 753 <property name="sizePolicy"> 754 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 755 <horstretch>0</horstretch> 756 <verstretch>0</verstretch> 757 </sizepolicy> 758 </property> 759 <property name="toolTip"> 760 <string><html><head/><body><p>Minimum, Optimum, and Maximum lengths (in bases) of a primer oligo.</p><p>Primer3 will not pick primers shorter than Min or longer than Max, and with default arguments will attempt to pick primers close with size close to Opt.</p><p>Min cannot be smaller than 1. Max cannot be larger than 36. (This limit is governed by maximum oligo size for which melting-temperature calculations are valid.)</p><p>Min cannot be greater than Max.</p></body></html></string> 761 </property> 762 </widget> 763 </item> 764 <item row="1" column="5"> 765 <widget class="QDoubleSpinBox" name="edit_PRIMER_OPT_TM"> 766 <property name="sizePolicy"> 767 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 768 <horstretch>0</horstretch> 769 <verstretch>0</verstretch> 770 </sizepolicy> 771 </property> 772 <property name="toolTip"> 773 <string><html><head/><body><p>Minimum, Optimum, and Maximum melting temperatures (Celsius) for a primer oligo.</p><p>Primer3 will not pick oligos with temperatures smaller than Min or larger than Max, and with default conditions will try to pick primers with melting temperatures close to Opt.</p></body></html></string> 774 </property> 775 <property name="maximum"> 776 <double>9999.989999999999782</double> 777 </property> 778 </widget> 779 </item> 780 <item row="1" column="7"> 781 <widget class="QDoubleSpinBox" name="edit_PRIMER_MAX_TM"> 782 <property name="sizePolicy"> 783 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 784 <horstretch>0</horstretch> 785 <verstretch>0</verstretch> 786 </sizepolicy> 787 </property> 788 <property name="toolTip"> 789 <string><html><head/><body><p>Minimum, Optimum, and Maximum melting temperatures (Celsius) for a primer oligo.</p><p>Primer3 will not pick oligos with temperatures smaller than Min or larger than Max, and with default conditions will try to pick primers with melting temperatures close to Opt.</p></body></html></string> 790 </property> 791 <property name="maximum"> 792 <double>9999.989999999999782</double> 793 </property> 794 </widget> 795 </item> 796 <item row="1" column="3"> 797 <widget class="QDoubleSpinBox" name="edit_PRIMER_MIN_TM"> 798 <property name="sizePolicy"> 799 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 800 <horstretch>0</horstretch> 801 <verstretch>0</verstretch> 802 </sizepolicy> 803 </property> 804 <property name="toolTip"> 805 <string><html><head/><body><p>Minimum, Optimum, and Maximum melting temperatures (Celsius) for a primer oligo.</p><p>Primer3 will not pick oligos with temperatures smaller than Min or larger than Max, and with default conditions will try to pick primers with melting temperatures close to Opt.</p></body></html></string> 806 </property> 807 <property name="maximum"> 808 <double>9999.989999999999782</double> 809 </property> 810 </widget> 811 </item> 812 <item row="3" column="3"> 813 <widget class="QDoubleSpinBox" name="edit_PRIMER_MIN_GC"> 814 <property name="sizePolicy"> 815 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 816 <horstretch>0</horstretch> 817 <verstretch>0</verstretch> 818 </sizepolicy> 819 </property> 820 <property name="toolTip"> 821 <string><html><head/><body><p>Minimum, Optimum, and Maximum percentage of Gs and Cs in any primer or oligo.</p></body></html> 822</string> 823 </property> 824 <property name="maximum"> 825 <double>100.000000000000000</double> 826 </property> 827 </widget> 828 </item> 829 <item row="3" column="7"> 830 <widget class="QDoubleSpinBox" name="edit_PRIMER_MAX_GC"> 831 <property name="sizePolicy"> 832 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 833 <horstretch>0</horstretch> 834 <verstretch>0</verstretch> 835 </sizepolicy> 836 </property> 837 <property name="toolTip"> 838 <string><html><head/><body><p>Minimum, Optimum, and Maximum percentage of Gs and Cs in any primer or oligo.</p></body></html></string> 839 </property> 840 <property name="maximum"> 841 <double>100.000000000000000</double> 842 </property> 843 </widget> 844 </item> 845 <item row="2" column="3"> 846 <widget class="QLineEdit" name="edit_PRIMER_PRODUCT_MIN_TM"> 847 <property name="toolTip"> 848 <string><html><head/><body><p>The minimum, optimum, and maximum melting temperature of the amplicon.</p><p>Primer3 will not pick a product with melting temperature less than min or greater than max. If Opt is supplied and the Penalty Weights for Product Size are non-0 Primer3 will attempt to pick an amplicon with melting temperature close to Opt.</p></body></html></string> 849 </property> 850 </widget> 851 </item> 852 <item row="2" column="5"> 853 <widget class="QLineEdit" name="edit_PRIMER_PRODUCT_OPT_TM"> 854 <property name="toolTip"> 855 <string><html><head/><body><p>The minimum, optimum, and maximum melting temperature of the amplicon.</p><p>Primer3 will not pick a product with melting temperature less than min or greater than max. If Opt is supplied and the Penalty Weights for Product Size are non-0 Primer3 will attempt to pick an amplicon with melting temperature close to Opt.</p></body></html></string> 856 </property> 857 </widget> 858 </item> 859 <item row="2" column="7"> 860 <widget class="QLineEdit" name="edit_PRIMER_PRODUCT_MAX_TM"> 861 <property name="toolTip"> 862 <string><html><head/><body><p>The minimum, optimum, and maximum melting temperature of the amplicon.</p><p>Primer3 will not pick a product with melting temperature less than min or greater than max. If Opt is supplied and the Penalty Weights for Product Size are non-0 Primer3 will attempt to pick an amplicon with melting temperature close to Opt.</p></body></html></string> 863 </property> 864 </widget> 865 </item> 866 <item row="3" column="5"> 867 <widget class="QLineEdit" name="edit_PRIMER_OPT_GC_PERCENT"> 868 <property name="toolTip"> 869 <string><html><head/><body><p>Minimum, Optimum, and Maximum percentage of Gs and Cs in any primer or oligo.</p></body></html></string> 870 </property> 871 </widget> 872 </item> 873 <item row="3" column="10"> 874 <spacer name="horizontalSpacer_13"> 875 <property name="orientation"> 876 <enum>Qt::Horizontal</enum> 877 </property> 878 <property name="sizeHint" stdset="0"> 879 <size> 880 <width>40</width> 881 <height>20</height> 882 </size> 883 </property> 884 </spacer> 885 </item> 886 <item row="0" column="10"> 887 <spacer name="horizontalSpacer_15"> 888 <property name="orientation"> 889 <enum>Qt::Horizontal</enum> 890 </property> 891 <property name="sizeHint" stdset="0"> 892 <size> 893 <width>40</width> 894 <height>20</height> 895 </size> 896 </property> 897 </spacer> 898 </item> 899 <item row="0" column="11"> 900 <spacer name="horizontalSpacer_21"> 901 <property name="orientation"> 902 <enum>Qt::Horizontal</enum> 903 </property> 904 <property name="sizeHint" stdset="0"> 905 <size> 906 <width>40</width> 907 <height>20</height> 908 </size> 909 </property> 910 </spacer> 911 </item> 912 <item row="3" column="11"> 913 <spacer name="horizontalSpacer_19"> 914 <property name="orientation"> 915 <enum>Qt::Horizontal</enum> 916 </property> 917 <property name="sizeHint" stdset="0"> 918 <size> 919 <width>40</width> 920 <height>20</height> 921 </size> 922 </property> 923 </spacer> 924 </item> 925 <item row="2" column="11"> 926 <spacer name="horizontalSpacer_20"> 927 <property name="orientation"> 928 <enum>Qt::Horizontal</enum> 929 </property> 930 <property name="sizeHint" stdset="0"> 931 <size> 932 <width>40</width> 933 <height>20</height> 934 </size> 935 </property> 936 </spacer> 937 </item> 938 <item row="2" column="8"> 939 <spacer name="horizontalSpacer_11"> 940 <property name="orientation"> 941 <enum>Qt::Horizontal</enum> 942 </property> 943 <property name="sizeHint" stdset="0"> 944 <size> 945 <width>40</width> 946 <height>20</height> 947 </size> 948 </property> 949 </spacer> 950 </item> 951 <item row="2" column="9"> 952 <widget class="QLabel" name="label_PRIMER_MAX_DIFF_TM"> 953 <property name="text"> 954 <string>Max Tm difference</string> 955 </property> 956 </widget> 957 </item> 958 <item row="2" column="10"> 959 <widget class="QDoubleSpinBox" name="edit_PRIMER_MAX_DIFF_TM"> 960 <property name="sizePolicy"> 961 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 962 <horstretch>0</horstretch> 963 <verstretch>0</verstretch> 964 </sizepolicy> 965 </property> 966 <property name="toolTip"> 967 <string><html><head/><body><p>Maximum acceptable (unsigned) difference between the melting temperatures of the left and right primers.</p></body></html></string> 968 </property> 969 <property name="maximum"> 970 <double>9999.989999999999782</double> 971 </property> 972 </widget> 973 </item> 974 <item row="1" column="9"> 975 <widget class="QLabel" name="label_PRIMER_TM_SANTALUCIA"> 976 <property name="text"> 977 <string>Table of thermodynamic parameters</string> 978 </property> 979 </widget> 980 </item> 981 <item row="1" column="10"> 982 <widget class="QComboBox" name="combobox_PRIMER_TM_SANTALUCIA"> 983 <property name="enabled"> 984 <bool>true</bool> 985 </property> 986 <property name="toolTip"> 987 <string><html><head/><body><p>Specifies details of melting temperature calculation.</p><p>First method uses the table of thermodynamic parameters from the paper [Breslauer KJ, et. al (1986), Proc Natl Acad Sci 83:4746-50 http://dx.doi.org/10.1073/pnas.83.11.3746]</p><p>Second method (recommended) was suggested in the paper [SantaLucia JR (1998), Proc Natl Acad Sci 95:1460-65 http://dx.doi.org/10.1073/pnas.95.4.1460].</p></body></html></string> 988 </property> 989 <item> 990 <property name="text"> 991 <string>SantaLucia 1998</string> 992 </property> 993 </item> 994 <item> 995 <property name="text"> 996 <string>Breslauer et. al 1986</string> 997 </property> 998 </item> 999 </widget> 1000 </item> 1001 </layout> 1002 </item> 1003 <item> 1004 <widget class="Line" name="line_2"> 1005 <property name="orientation"> 1006 <enum>Qt::Horizontal</enum> 1007 </property> 1008 </widget> 1009 </item> 1010 <item> 1011 <layout class="QGridLayout" name="gridLayout_13"> 1012 <item row="0" column="0"> 1013 <widget class="QLabel" name="label_PRIMER_SELF_ANY"> 1014 <property name="text"> 1015 <string>Max self complementarity</string> 1016 </property> 1017 </widget> 1018 </item> 1019 <item row="0" column="2"> 1020 <widget class="QLabel" name="label_PRIMER_SELF_END"> 1021 <property name="text"> 1022 <string>Max 3' self complementarity</string> 1023 </property> 1024 </widget> 1025 </item> 1026 <item row="2" column="0"> 1027 <widget class="QLabel" name="label_PRIMER_INSIDE_PENALTY"> 1028 <property name="text"> 1029 <string>Inside target penalty</string> 1030 </property> 1031 </widget> 1032 </item> 1033 <item row="2" column="2"> 1034 <widget class="QLabel" name="label_PRIMER_OUTSIDE_PENALTY"> 1035 <property name="text"> 1036 <string>Outside target penalty</string> 1037 </property> 1038 </widget> 1039 </item> 1040 <item row="4" column="0"> 1041 <widget class="QLabel" name="label_PRIMER_SALT_CONC"> 1042 <property name="text"> 1043 <string>Concentration of monovalent cations</string> 1044 </property> 1045 </widget> 1046 </item> 1047 <item row="1" column="0"> 1048 <widget class="QLabel" name="label_PRIMER_NUM_NS_ACCEPTED"> 1049 <property name="text"> 1050 <string>Max #N's</string> 1051 </property> 1052 </widget> 1053 </item> 1054 <item row="1" column="2"> 1055 <widget class="QLabel" name="label_PRIMER_MAX_POLY_X"> 1056 <property name="text"> 1057 <string>Max poly-X</string> 1058 </property> 1059 </widget> 1060 </item> 1061 <item row="3" column="0"> 1062 <widget class="QLabel" name="label_PRIMER_FIRST_BASE_INDEX"> 1063 <property name="text"> 1064 <string>First base index</string> 1065 </property> 1066 </widget> 1067 </item> 1068 <item row="3" column="2"> 1069 <widget class="QLabel" name="label_PRIMER_GC_CLAMP"> 1070 <property name="text"> 1071 <string>CG clamp</string> 1072 </property> 1073 </widget> 1074 </item> 1075 <item row="5" column="0"> 1076 <widget class="QLabel" name="label_PRIMER_DIVALENT_CONC"> 1077 <property name="text"> 1078 <string>Concentration of divalent cations</string> 1079 </property> 1080 </widget> 1081 </item> 1082 <item row="4" column="2"> 1083 <widget class="QLabel" name="label_PRIMER_SALT_CORRECTIONS"> 1084 <property name="text"> 1085 <string>Salt correction formula</string> 1086 </property> 1087 </widget> 1088 </item> 1089 <item row="4" column="3"> 1090 <widget class="QComboBox" name="combobox_PRIMER_SALT_CORRECTIONS"> 1091 <property name="enabled"> 1092 <bool>true</bool> 1093 </property> 1094 <property name="toolTip"> 1095 <string><html><head/><body><p>Specifies the salt correction formula for the melting temperature calculation.</p></body></html></string> 1096 </property> 1097 <item> 1098 <property name="text"> 1099 <string>SantaLucia 1998</string> 1100 </property> 1101 </item> 1102 <item> 1103 <property name="text"> 1104 <string>Schildkraut and Lifson 1965</string> 1105 </property> 1106 </item> 1107 <item> 1108 <property name="text"> 1109 <string>Owczarzy et. 2004</string> 1110 </property> 1111 </item> 1112 </widget> 1113 </item> 1114 <item row="5" column="2"> 1115 <widget class="QLabel" name="label_PRIMER_DNTP_CONC"> 1116 <property name="text"> 1117 <string>Concentration of dNTPs</string> 1118 </property> 1119 </widget> 1120 </item> 1121 <item row="6" column="0"> 1122 <widget class="QLabel" name="label_PRIMER_DNA_CONC"> 1123 <property name="text"> 1124 <string>Annealing oligo concentration</string> 1125 </property> 1126 </widget> 1127 </item> 1128 <item row="6" column="2"> 1129 <spacer name="horizontalSpacer_22"> 1130 <property name="orientation"> 1131 <enum>Qt::Horizontal</enum> 1132 </property> 1133 <property name="sizeHint" stdset="0"> 1134 <size> 1135 <width>40</width> 1136 <height>20</height> 1137 </size> 1138 </property> 1139 </spacer> 1140 </item> 1141 <item row="5" column="4"> 1142 <spacer name="horizontalSpacer_23"> 1143 <property name="orientation"> 1144 <enum>Qt::Horizontal</enum> 1145 </property> 1146 <property name="sizeHint" stdset="0"> 1147 <size> 1148 <width>40</width> 1149 <height>20</height> 1150 </size> 1151 </property> 1152 </spacer> 1153 </item> 1154 <item row="4" column="4"> 1155 <spacer name="horizontalSpacer_24"> 1156 <property name="orientation"> 1157 <enum>Qt::Horizontal</enum> 1158 </property> 1159 <property name="sizeHint" stdset="0"> 1160 <size> 1161 <width>40</width> 1162 <height>20</height> 1163 </size> 1164 </property> 1165 </spacer> 1166 </item> 1167 <item row="3" column="4"> 1168 <spacer name="horizontalSpacer_26"> 1169 <property name="orientation"> 1170 <enum>Qt::Horizontal</enum> 1171 </property> 1172 <property name="sizeHint" stdset="0"> 1173 <size> 1174 <width>40</width> 1175 <height>20</height> 1176 </size> 1177 </property> 1178 </spacer> 1179 </item> 1180 <item row="1" column="4"> 1181 <spacer name="horizontalSpacer_27"> 1182 <property name="orientation"> 1183 <enum>Qt::Horizontal</enum> 1184 </property> 1185 <property name="sizeHint" stdset="0"> 1186 <size> 1187 <width>40</width> 1188 <height>20</height> 1189 </size> 1190 </property> 1191 </spacer> 1192 </item> 1193 <item row="0" column="4"> 1194 <spacer name="horizontalSpacer_32"> 1195 <property name="orientation"> 1196 <enum>Qt::Horizontal</enum> 1197 </property> 1198 <property name="sizeHint" stdset="0"> 1199 <size> 1200 <width>40</width> 1201 <height>20</height> 1202 </size> 1203 </property> 1204 </spacer> 1205 </item> 1206 <item row="6" column="3"> 1207 <spacer name="horizontalSpacer_25"> 1208 <property name="orientation"> 1209 <enum>Qt::Horizontal</enum> 1210 </property> 1211 <property name="sizeHint" stdset="0"> 1212 <size> 1213 <width>40</width> 1214 <height>20</height> 1215 </size> 1216 </property> 1217 </spacer> 1218 </item> 1219 <item row="2" column="4"> 1220 <spacer name="horizontalSpacer_34"> 1221 <property name="orientation"> 1222 <enum>Qt::Horizontal</enum> 1223 </property> 1224 <property name="sizeHint" stdset="0"> 1225 <size> 1226 <width>40</width> 1227 <height>20</height> 1228 </size> 1229 </property> 1230 </spacer> 1231 </item> 1232 <item row="6" column="4"> 1233 <spacer name="horizontalSpacer_35"> 1234 <property name="orientation"> 1235 <enum>Qt::Horizontal</enum> 1236 </property> 1237 <property name="sizeHint" stdset="0"> 1238 <size> 1239 <width>40</width> 1240 <height>20</height> 1241 </size> 1242 </property> 1243 </spacer> 1244 </item> 1245 <item row="0" column="3"> 1246 <widget class="QDoubleSpinBox" name="edit_PRIMER_SELF_END"> 1247 <property name="sizePolicy"> 1248 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 1249 <horstretch>0</horstretch> 1250 <verstretch>0</verstretch> 1251 </sizepolicy> 1252 </property> 1253 <property name="toolTip"> 1254 <string><html><head/><body><p>The maximum allowable 3'-anchored global alignment score when testing a single primer for self-complementarity, and the maximum allowable 3'-anchored global alignment score when testing for complementarity between left and right primers.</p></body></html></string> 1255 </property> 1256 <property name="maximum"> 1257 <double>9999.989999999999782</double> 1258 </property> 1259 </widget> 1260 </item> 1261 <item row="0" column="1"> 1262 <widget class="QDoubleSpinBox" name="edit_PRIMER_SELF_ANY"> 1263 <property name="sizePolicy"> 1264 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 1265 <horstretch>0</horstretch> 1266 <verstretch>0</verstretch> 1267 </sizepolicy> 1268 </property> 1269 <property name="toolTip"> 1270 <string><html><head/><body><p>The maximum allowable local alignment score when testing a single primer for (local) self-complementarity and the maximum allowable local alignment score when testing for complementarity between left and right primers.</p><p>Local self-complementarity is taken to predict the tendency of primers to anneal to each other without necessarily causing self-priming in the PCR. The scoring system gives 1.00 for complementary bases, -0.25 for a match of any base (or N) with an N, -1.00 for a mismatch, and -2.00 for a gap. Only single-base-pair gaps are allowed.</p></body></html></string> 1271 </property> 1272 <property name="maximum"> 1273 <double>9999.989999999999782</double> 1274 </property> 1275 </widget> 1276 </item> 1277 <item row="1" column="1"> 1278 <widget class="QSpinBox" name="edit_PRIMER_NUM_NS_ACCEPTED"> 1279 <property name="sizePolicy"> 1280 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 1281 <horstretch>0</horstretch> 1282 <verstretch>0</verstretch> 1283 </sizepolicy> 1284 </property> 1285 <property name="toolTip"> 1286 <string><html><head/><body><p>Maximum number of unknown bases (N) allowable in any primer.</p></body></html></string> 1287 </property> 1288 <property name="maximum"> 1289 <number>9999999</number> 1290 </property> 1291 </widget> 1292 </item> 1293 <item row="1" column="3"> 1294 <widget class="QSpinBox" name="edit_PRIMER_MAX_POLY_X"> 1295 <property name="sizePolicy"> 1296 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 1297 <horstretch>0</horstretch> 1298 <verstretch>0</verstretch> 1299 </sizepolicy> 1300 </property> 1301 <property name="toolTip"> 1302 <string><html><head/><body><p>The maximum allowable length of a mononucleotide repeat, for example AAAAAA.</p></body></html></string> 1303 </property> 1304 <property name="maximum"> 1305 <number>9999999</number> 1306 </property> 1307 </widget> 1308 </item> 1309 <item row="2" column="3"> 1310 <widget class="QDoubleSpinBox" name="edit_PRIMER_OUTSIDE_PENALTY"> 1311 <property name="sizePolicy"> 1312 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 1313 <horstretch>0</horstretch> 1314 <verstretch>0</verstretch> 1315 </sizepolicy> 1316 </property> 1317 <property name="toolTip"> 1318 <string><html><head/><body><p>Non-default values valid only for sequences with 0 or 1 target regions.</p><p>If the primer is part of a pair that spans a target and does not overlap the target, then multiply this value times the number of nucleotide positions from the 3' end to the (unique) target to get the 'position penalty'. The effect of this parameter is to allow Primer3 to include nearness to the target as a term in the objective function.</p></body></html></string> 1319 </property> 1320 <property name="maximum"> 1321 <double>9999.989999999999782</double> 1322 </property> 1323 </widget> 1324 </item> 1325 <item row="3" column="1"> 1326 <widget class="QSpinBox" name="edit_PRIMER_FIRST_BASE_INDEX"> 1327 <property name="sizePolicy"> 1328 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 1329 <horstretch>0</horstretch> 1330 <verstretch>0</verstretch> 1331 </sizepolicy> 1332 </property> 1333 <property name="toolTip"> 1334 <string><html><head/><body><p>This parameter is the index of the first base in the input sequence.</p></body></html></string> 1335 </property> 1336 <property name="maximum"> 1337 <number>9999999</number> 1338 </property> 1339 </widget> 1340 </item> 1341 <item row="3" column="3"> 1342 <widget class="QSpinBox" name="edit_PRIMER_GC_CLAMP"> 1343 <property name="sizePolicy"> 1344 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 1345 <horstretch>0</horstretch> 1346 <verstretch>0</verstretch> 1347 </sizepolicy> 1348 </property> 1349 <property name="toolTip"> 1350 <string><html><head/><body><p>Require the specified number of consecutive Gs and Cs at the 3' end of both the left and right primer.</p><p>This parameter has no effect on the internal oligo if one is requested.</p></body></html></string> 1351 </property> 1352 <property name="maximum"> 1353 <number>9999999</number> 1354 </property> 1355 </widget> 1356 </item> 1357 <item row="4" column="1"> 1358 <widget class="QDoubleSpinBox" name="edit_PRIMER_SALT_CONC"> 1359 <property name="sizePolicy"> 1360 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 1361 <horstretch>0</horstretch> 1362 <verstretch>0</verstretch> 1363 </sizepolicy> 1364 </property> 1365 <property name="toolTip"> 1366 <string><html><head/><body><p>The millimolar (mM) concentration of monovalent salt cations (usually KCl) in the PCR.</p><p>Primer3 uses this argument to calculate oligo and primer melting temperatures.</p></body></html></string> 1367 </property> 1368 <property name="maximum"> 1369 <double>9999.989999999999782</double> 1370 </property> 1371 </widget> 1372 </item> 1373 <item row="5" column="1"> 1374 <widget class="QDoubleSpinBox" name="edit_PRIMER_DIVALENT_CONC"> 1375 <property name="sizePolicy"> 1376 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 1377 <horstretch>0</horstretch> 1378 <verstretch>0</verstretch> 1379 </sizepolicy> 1380 </property> 1381 <property name="toolTip"> 1382 <string><html><head/><body><p>The millimolar concentration of divalent salt cations (usually MgCl^(2+)) in the PCR.</p><p>Primer3 converts concentration of divalent cations to concentration of monovalent cations using following formula:</p><p><span style=" font-weight:600;">[Monovalent cations] = [Monovalent cations] + 120*(([divalent cations] - [dNTP])^0.5)</span></p><p>In addition, if the specified concentration of dNTPs is larger than the concentration of divalent cations then the effect of the divalent cations is not considered.</p></body></html></string> 1383 </property> 1384 </widget> 1385 </item> 1386 <item row="5" column="3"> 1387 <widget class="QDoubleSpinBox" name="edit_PRIMER_DNTP_CONC"> 1388 <property name="sizePolicy"> 1389 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 1390 <horstretch>0</horstretch> 1391 <verstretch>0</verstretch> 1392 </sizepolicy> 1393 </property> 1394 <property name="toolTip"> 1395 <string><html><head/><body><p>The millimolar concentration of the sum of all deoxyribonucleotide triphosphates.</p></body></html></string> 1396 </property> 1397 </widget> 1398 </item> 1399 <item row="6" column="1"> 1400 <widget class="QDoubleSpinBox" name="edit_PRIMER_DNA_CONC"> 1401 <property name="sizePolicy"> 1402 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 1403 <horstretch>0</horstretch> 1404 <verstretch>0</verstretch> 1405 </sizepolicy> 1406 </property> 1407 <property name="toolTip"> 1408 <string><html><head/><body><p>A value to use as nanomolar (nM) concentration of each annealing oligo over the course the PCR.</p><p>Primer3 uses this argument to esimate oligo melting temperatures.</p><p>The default (50nM) works well with the standard protocol used at the Whitehead/MIT Center for Genome Research --0.5 microliters of 20 micromolar concentration for each primer in a 20 microliter reaction with 10 nanograms template, 0.025 units/microliter Taq polymerase in 0.1 mM each dNTP, 1.5mM MgCl2, 50mM KCl, 10mM Tris-HCL (pH 9.3) using 35 cycles with an annealing temperature of 56 degrees Celsius.</p><p>The value of this parameter is less than the actual concentration of oligos in the initial reaction mix because it is the concentration of annealing oligos, which in turn depends on the amount of template (including PCR product) in a given cycle. This concentration increases a great deal during a PCR; fortunately PCR seems quite robust for a variety of oligo melting temperatures.</p></body></html></string> 1409 </property> 1410 </widget> 1411 </item> 1412 <item row="2" column="1"> 1413 <widget class="QLineEdit" name="edit_PRIMER_INSIDE_PENALTY"> 1414 <property name="toolTip"> 1415 <string><html><head/><body><p>Non-default values valid only for sequences with 0 or 1 target regions.</p><p>If the primer is part of a pair that spans a target and overlaps the target, then multiply this value times the number of nucleotide positions by which the primer overlaps the (unique) target to get the 'position penalty'.</p><p>The effect of this parameter is to allow Primer3 to include overlap with the target as a term in the objective function.</p></body></html></string> 1416 </property> 1417 </widget> 1418 </item> 1419 </layout> 1420 </item> 1421 <item> 1422 <widget class="Line" name="line_4"> 1423 <property name="orientation"> 1424 <enum>Qt::Horizontal</enum> 1425 </property> 1426 </widget> 1427 </item> 1428 <item> 1429 <layout class="QHBoxLayout" name="horizontalLayout_16"> 1430 <item> 1431 <widget class="QCheckBox" name="checkbox_PRIMER_LIBERAL_BASE"> 1432 <property name="text"> 1433 <string> Liberal base</string> 1434 </property> 1435 <property name="checked"> 1436 <bool>true</bool> 1437 </property> 1438 </widget> 1439 </item> 1440 <item> 1441 <widget class="QCheckBox" name="checkbox_SHOW_DEBUGGING"> 1442 <property name="enabled"> 1443 <bool>false</bool> 1444 </property> 1445 <property name="text"> 1446 <string>Show debugging info</string> 1447 </property> 1448 </widget> 1449 </item> 1450 <item> 1451 <widget class="QCheckBox" name="checkbox_PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS"> 1452 <property name="text"> 1453 <string>Do not treat ambiguity codes in libraries as consensus</string> 1454 </property> 1455 <property name="checked"> 1456 <bool>true</bool> 1457 </property> 1458 </widget> 1459 </item> 1460 <item> 1461 <widget class="QCheckBox" name="checkbox_PRIMER_LOWERCASE_MASKING"> 1462 <property name="text"> 1463 <string>Lowercase masking</string> 1464 </property> 1465 </widget> 1466 </item> 1467 </layout> 1468 </item> 1469 </layout> 1470 </widget> 1471 <widget class="QWidget" name="tab_InternalOligo"> 1472 <attribute name="title"> 1473 <string>Internal Oligo</string> 1474 </attribute> 1475 <attribute name="toolTip"> 1476 <string><html><head/><body><p>Parameters governing choice of internal oligos are analogous to the parameters governing choice of primer pairs.</p></body></html></string> 1477 </attribute> 1478 <layout class="QVBoxLayout" name="verticalLayout_7"> 1479 <item> 1480 <layout class="QHBoxLayout" name="horizontalLayout_4"> 1481 <item> 1482 <widget class="QLabel" name="label_58"> 1483 <property name="text"> 1484 <string>Hyb oligo excluded region</string> 1485 </property> 1486 </widget> 1487 </item> 1488 <item> 1489 <widget class="QLineEdit" name="edit_PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION"> 1490 <property name="toolTip"> 1491 <string><html><head/><body><p>Middle oligos may not overlap any region specified by this tag. The associated value must be a space-separated list of</p><p><span style=" font-weight:600;">&lt;start&gt;,&lt;length&gt;</span></p><p>pairs, where &lt;start&gt; is the index of the first base of an excluded region, and &lt;length&gt; is its length. Often one would make Target regions excluded regions for internal oligos.</p></body></html></string> 1492 </property> 1493 </widget> 1494 </item> 1495 </layout> 1496 </item> 1497 <item> 1498 <widget class="Line" name="line_9"> 1499 <property name="orientation"> 1500 <enum>Qt::Horizontal</enum> 1501 </property> 1502 </widget> 1503 </item> 1504 <item> 1505 <layout class="QGridLayout" name="gridLayout_14"> 1506 <item row="0" column="0"> 1507 <widget class="QLabel" name="label_59"> 1508 <property name="text"> 1509 <string>Hyb oligo size</string> 1510 </property> 1511 </widget> 1512 </item> 1513 <item row="1" column="0"> 1514 <widget class="QLabel" name="label_60"> 1515 <property name="text"> 1516 <string>Hyb oligo Tm</string> 1517 </property> 1518 </widget> 1519 </item> 1520 <item row="2" column="0"> 1521 <widget class="QLabel" name="label_61"> 1522 <property name="text"> 1523 <string>Hyb oligo GC%</string> 1524 </property> 1525 </widget> 1526 </item> 1527 <item row="0" column="1"> 1528 <widget class="QLabel" name="label_62"> 1529 <property name="text"> 1530 <string>Min:</string> 1531 </property> 1532 </widget> 1533 </item> 1534 <item row="1" column="1"> 1535 <widget class="QLabel" name="label_63"> 1536 <property name="text"> 1537 <string>Min:</string> 1538 </property> 1539 </widget> 1540 </item> 1541 <item row="2" column="1"> 1542 <widget class="QLabel" name="label_64"> 1543 <property name="text"> 1544 <string>Min:</string> 1545 </property> 1546 </widget> 1547 </item> 1548 <item row="0" column="2"> 1549 <widget class="QSpinBox" name="edit_PRIMER_INTERNAL_OLIGO_MIN_SIZE"> 1550 <property name="sizePolicy"> 1551 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 1552 <horstretch>0</horstretch> 1553 <verstretch>0</verstretch> 1554 </sizepolicy> 1555 </property> 1556 <property name="toolTip"> 1557 <string><html><head/><body><p>Equivalent parameter of Primer Size for the internal oligo.</p></body></html></string> 1558 </property> 1559 <property name="maximum"> 1560 <number>9999</number> 1561 </property> 1562 </widget> 1563 </item> 1564 <item row="1" column="2"> 1565 <widget class="QDoubleSpinBox" name="edit_PRIMER_INTERNAL_OLIGO_MIN_TM"> 1566 <property name="sizePolicy"> 1567 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 1568 <horstretch>0</horstretch> 1569 <verstretch>0</verstretch> 1570 </sizepolicy> 1571 </property> 1572 <property name="toolTip"> 1573 <string><html><head/><body><p>Equivalent parameter of Primer Tm for the internal oligo.</p></body></html></string> 1574 </property> 1575 <property name="maximum"> 1576 <double>9999.989999999999782</double> 1577 </property> 1578 </widget> 1579 </item> 1580 <item row="2" column="2"> 1581 <widget class="QDoubleSpinBox" name="edit_PRIMER_INTERNAL_OLIGO_MIN_GC"> 1582 <property name="sizePolicy"> 1583 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 1584 <horstretch>0</horstretch> 1585 <verstretch>0</verstretch> 1586 </sizepolicy> 1587 </property> 1588 <property name="toolTip"> 1589 <string><html><head/><body><p>Equivalent parameter of primer GC% for the internal oligo.</p></body></html></string> 1590 </property> 1591 <property name="maximum"> 1592 <double>100.000000000000000</double> 1593 </property> 1594 </widget> 1595 </item> 1596 <item row="0" column="3"> 1597 <widget class="QLabel" name="label_65"> 1598 <property name="text"> 1599 <string>Opt:</string> 1600 </property> 1601 </widget> 1602 </item> 1603 <item row="1" column="3"> 1604 <widget class="QLabel" name="label_66"> 1605 <property name="text"> 1606 <string>Opt:</string> 1607 </property> 1608 </widget> 1609 </item> 1610 <item row="2" column="3"> 1611 <widget class="QLabel" name="label_67"> 1612 <property name="text"> 1613 <string>Opt:</string> 1614 </property> 1615 </widget> 1616 </item> 1617 <item row="0" column="4"> 1618 <widget class="QSpinBox" name="edit_PRIMER_INTERNAL_OLIGO_OPT_SIZE"> 1619 <property name="sizePolicy"> 1620 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 1621 <horstretch>0</horstretch> 1622 <verstretch>0</verstretch> 1623 </sizepolicy> 1624 </property> 1625 <property name="toolTip"> 1626 <string><html><head/><body><p>Equivalent parameter of Primer Size for the internal oligo.</p></body></html></string> 1627 </property> 1628 <property name="maximum"> 1629 <number>9999</number> 1630 </property> 1631 </widget> 1632 </item> 1633 <item row="1" column="4"> 1634 <widget class="QDoubleSpinBox" name="edit_PRIMER_INTERNAL_OLIGO_OPT_TM"> 1635 <property name="sizePolicy"> 1636 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 1637 <horstretch>0</horstretch> 1638 <verstretch>0</verstretch> 1639 </sizepolicy> 1640 </property> 1641 <property name="toolTip"> 1642 <string><html><head/><body><p>Equivalent parameter of Primer Tm for the internal oligo.</p></body></html></string> 1643 </property> 1644 <property name="maximum"> 1645 <double>9999.989999999999782</double> 1646 </property> 1647 </widget> 1648 </item> 1649 <item row="2" column="4"> 1650 <widget class="QLineEdit" name="edit_PRIMER_INTERNAL_OLIGO_OPT_GC_PERCENT"> 1651 <property name="toolTip"> 1652 <string><html><head/><body><p>Equivalent parameter of Primer GC% for the internal oligo.</p></body></html></string> 1653 </property> 1654 </widget> 1655 </item> 1656 <item row="0" column="5"> 1657 <widget class="QLabel" name="label_68"> 1658 <property name="text"> 1659 <string>Max:</string> 1660 </property> 1661 </widget> 1662 </item> 1663 <item row="1" column="5"> 1664 <widget class="QLabel" name="label_69"> 1665 <property name="text"> 1666 <string>Max:</string> 1667 </property> 1668 </widget> 1669 </item> 1670 <item row="2" column="5"> 1671 <widget class="QLabel" name="label_70"> 1672 <property name="text"> 1673 <string>Max:</string> 1674 </property> 1675 </widget> 1676 </item> 1677 <item row="0" column="6"> 1678 <widget class="QSpinBox" name="edit_PRIMER_INTERNAL_OLIGO_MAX_SIZE"> 1679 <property name="sizePolicy"> 1680 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 1681 <horstretch>0</horstretch> 1682 <verstretch>0</verstretch> 1683 </sizepolicy> 1684 </property> 1685 <property name="toolTip"> 1686 <string><html><head/><body><p>Equivalent parameter of Primer Size for the internal oligo.</p></body></html></string> 1687 </property> 1688 </widget> 1689 </item> 1690 <item row="1" column="6"> 1691 <widget class="QDoubleSpinBox" name="edit_PRIMER_INTERNAL_OLIGO_MAX_TM"> 1692 <property name="sizePolicy"> 1693 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 1694 <horstretch>0</horstretch> 1695 <verstretch>0</verstretch> 1696 </sizepolicy> 1697 </property> 1698 <property name="toolTip"> 1699 <string><html><head/><body><p>Equivalent parameter of Primer Tm for the internal oligo.</p></body></html></string> 1700 </property> 1701 </widget> 1702 </item> 1703 <item row="2" column="6"> 1704 <widget class="QDoubleSpinBox" name="edit_PRIMER_INTERNAL_OLIGO_MAX_GC"> 1705 <property name="sizePolicy"> 1706 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 1707 <horstretch>0</horstretch> 1708 <verstretch>0</verstretch> 1709 </sizepolicy> 1710 </property> 1711 <property name="toolTip"> 1712 <string><html><head/><body><p>Equivalent parameter of Primer GC% for the internal oligo.</p></body></html></string> 1713 </property> 1714 </widget> 1715 </item> 1716 </layout> 1717 </item> 1718 <item> 1719 <widget class="Line" name="line_10"> 1720 <property name="orientation"> 1721 <enum>Qt::Horizontal</enum> 1722 </property> 1723 </widget> 1724 </item> 1725 <item> 1726 <layout class="QGridLayout" name="gridLayout_15"> 1727 <item row="0" column="0"> 1728 <widget class="QLabel" name="label_71"> 1729 <property name="text"> 1730 <string>Hyb oligo self complementarity</string> 1731 </property> 1732 </widget> 1733 </item> 1734 <item row="1" column="0"> 1735 <widget class="QLabel" name="label_72"> 1736 <property name="text"> 1737 <string>Max #Ns</string> 1738 </property> 1739 </widget> 1740 </item> 1741 <item row="2" column="0"> 1742 <widget class="QLabel" name="label_73"> 1743 <property name="text"> 1744 <string>Hyb oligo mishyb library</string> 1745 </property> 1746 </widget> 1747 </item> 1748 <item row="3" column="0"> 1749 <widget class="QLabel" name="label_74"> 1750 <property name="text"> 1751 <string>Hyb oligo min sequence quality</string> 1752 </property> 1753 </widget> 1754 </item> 1755 <item row="4" column="0"> 1756 <widget class="QLabel" name="label_75"> 1757 <property name="text"> 1758 <string>Hyb oligo conc of monovalent cations</string> 1759 </property> 1760 </widget> 1761 </item> 1762 <item row="5" column="0"> 1763 <widget class="QLabel" name="label_76"> 1764 <property name="text"> 1765 <string>Hyb oligo conc of divalent cations</string> 1766 </property> 1767 </widget> 1768 </item> 1769 <item row="0" column="1"> 1770 <widget class="QDoubleSpinBox" name="edit_PRIMER_INTERNAL_OLIGO_SELF_ANY"> 1771 <property name="sizePolicy"> 1772 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 1773 <horstretch>0</horstretch> 1774 <verstretch>0</verstretch> 1775 </sizepolicy> 1776 </property> 1777 <property name="toolTip"> 1778 <string><html><head/><body><p>Equivalent parameter of primer max self complemntarity for the internal oligo.</p></body></html></string> 1779 </property> 1780 <property name="maximum"> 1781 <double>9999.989999999999782</double> 1782 </property> 1783 </widget> 1784 </item> 1785 <item row="1" column="1"> 1786 <widget class="QSpinBox" name="edit_PRIMER_INTERNAL_OLIGO_NUM_NS"> 1787 <property name="sizePolicy"> 1788 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 1789 <horstretch>0</horstretch> 1790 <verstretch>0</verstretch> 1791 </sizepolicy> 1792 </property> 1793 <property name="toolTip"> 1794 <string><html><head/><body><p>Equivalent parameter of primer max #Ns for the internal oligo.</p></body></html></string> 1795 </property> 1796 <property name="maximum"> 1797 <number>9999</number> 1798 </property> 1799 </widget> 1800 </item> 1801 <item row="2" column="1"> 1802 <widget class="QComboBox" name="combobox_PRIMER_INTERNAL_OLIGO_MISHYB_LIBRARY"> 1803 <property name="sizePolicy"> 1804 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 1805 <horstretch>0</horstretch> 1806 <verstretch>0</verstretch> 1807 </sizepolicy> 1808 </property> 1809 <property name="toolTip"> 1810 <string><html><head/><body><p>Similar to primer mispriming library, except that the event we seek to avoid is hybridization of the internal oligo to sequences in this library rather than priming from them.</p></body></html></string> 1811 </property> 1812 </widget> 1813 </item> 1814 <item row="3" column="1"> 1815 <widget class="QSpinBox" name="edit_PRIMER_INTERNAL_OLIGO_MIN_QUALITY"> 1816 <property name="sizePolicy"> 1817 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 1818 <horstretch>0</horstretch> 1819 <verstretch>0</verstretch> 1820 </sizepolicy> 1821 </property> 1822 <property name="toolTip"> 1823 <string><html><head/><body><p>Equivalent parameter of primer minimum quality for the internal oligo.</p></body></html></string> 1824 </property> 1825 <property name="maximum"> 1826 <number>9999</number> 1827 </property> 1828 </widget> 1829 </item> 1830 <item row="4" column="1"> 1831 <widget class="QDoubleSpinBox" name="edit_PRIMER_INTERNAL_OLIGO_SALT_CONC"> 1832 <property name="sizePolicy"> 1833 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 1834 <horstretch>0</horstretch> 1835 <verstretch>0</verstretch> 1836 </sizepolicy> 1837 </property> 1838 <property name="toolTip"> 1839 <string><html><head/><body><p>Equivalent parameter of primer concentration of monovalent cations for the internal oligo.</p></body></html></string> 1840 </property> 1841 <property name="maximum"> 1842 <double>9999.989999999999782</double> 1843 </property> 1844 </widget> 1845 </item> 1846 <item row="5" column="1"> 1847 <widget class="QDoubleSpinBox" name="edit_PRIMER_INTERNAL_OLIGO_DIVALENT_CONC"> 1848 <property name="sizePolicy"> 1849 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 1850 <horstretch>0</horstretch> 1851 <verstretch>0</verstretch> 1852 </sizepolicy> 1853 </property> 1854 <property name="toolTip"> 1855 <string><html><head/><body><p>Equivalent parameter of primer concentration of divalent cations for the internal oligo.</p></body></html></string> 1856 </property> 1857 <property name="maximum"> 1858 <double>9999.989999999999782</double> 1859 </property> 1860 </widget> 1861 </item> 1862 <item row="0" column="2"> 1863 <widget class="QLabel" name="label_77"> 1864 <property name="text"> 1865 <string>Hyb oligo max 3' self complementarity</string> 1866 </property> 1867 </widget> 1868 </item> 1869 <item row="1" column="2"> 1870 <widget class="QLabel" name="label_78"> 1871 <property name="text"> 1872 <string>Hyb oligo max poly-X</string> 1873 </property> 1874 </widget> 1875 </item> 1876 <item row="2" column="2"> 1877 <widget class="QLabel" name="label_79"> 1878 <property name="text"> 1879 <string>Hyb oligo max mishyb</string> 1880 </property> 1881 </widget> 1882 </item> 1883 <item row="0" column="3"> 1884 <widget class="QDoubleSpinBox" name="edit_PRIMER_INTERNAL_OLIGO_SELF_END"> 1885 <property name="sizePolicy"> 1886 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 1887 <horstretch>0</horstretch> 1888 <verstretch>0</verstretch> 1889 </sizepolicy> 1890 </property> 1891 <property name="toolTip"> 1892 <string><html><head/><body><p>Equivalent parameter of primer max 3' self complementarity for the internal oligo.</p></body></html></string> 1893 </property> 1894 <property name="maximum"> 1895 <double>9999.989999999999782</double> 1896 </property> 1897 </widget> 1898 </item> 1899 <item row="1" column="3"> 1900 <widget class="QSpinBox" name="edit_PRIMER_INTERNAL_OLIGO_MAX_POLY_X"> 1901 <property name="sizePolicy"> 1902 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 1903 <horstretch>0</horstretch> 1904 <verstretch>0</verstretch> 1905 </sizepolicy> 1906 </property> 1907 <property name="toolTip"> 1908 <string><html><head/><body><p>Equivalent parameter of primer max poly-X for the internal oligo.</p></body></html></string> 1909 </property> 1910 <property name="maximum"> 1911 <number>9999</number> 1912 </property> 1913 </widget> 1914 </item> 1915 <item row="2" column="3"> 1916 <widget class="QDoubleSpinBox" name="edit_PRIMER_INTERNAL_OLIGO_MAX_MISHYB"> 1917 <property name="sizePolicy"> 1918 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 1919 <horstretch>0</horstretch> 1920 <verstretch>0</verstretch> 1921 </sizepolicy> 1922 </property> 1923 <property name="toolTip"> 1924 <string><html><head/><body><p>Similar to primer max library mispriming.</p></body></html></string> 1925 </property> 1926 <property name="maximum"> 1927 <double>9999.989999999999782</double> 1928 </property> 1929 </widget> 1930 </item> 1931 <item row="5" column="2"> 1932 <widget class="QLabel" name="label_81"> 1933 <property name="text"> 1934 <string>Hyb oligo [dNTP]</string> 1935 </property> 1936 </widget> 1937 </item> 1938 <item row="4" column="2"> 1939 <widget class="QLabel" name="label_80"> 1940 <property name="text"> 1941 <string>Hyb oligo DNA concentration</string> 1942 </property> 1943 </widget> 1944 </item> 1945 <item row="5" column="3"> 1946 <widget class="QDoubleSpinBox" name="edit_PRIMER_INTERNAL_OLIGO_DNTP_CONC"> 1947 <property name="sizePolicy"> 1948 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 1949 <horstretch>0</horstretch> 1950 <verstretch>0</verstretch> 1951 </sizepolicy> 1952 </property> 1953 <property name="toolTip"> 1954 <string><html><head/><body><p>Equivalent parameter of primer concentration of the dNTPs for the internal oligo.</p></body></html></string> 1955 </property> 1956 <property name="maximum"> 1957 <double>9999.989999999999782</double> 1958 </property> 1959 </widget> 1960 </item> 1961 <item row="4" column="3"> 1962 <widget class="QDoubleSpinBox" name="edit_PRIMER_INTERNAL_OLIGO_DNA_CONC"> 1963 <property name="sizePolicy"> 1964 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 1965 <horstretch>0</horstretch> 1966 <verstretch>0</verstretch> 1967 </sizepolicy> 1968 </property> 1969 <property name="toolTip"> 1970 <string><html><head/><body><p>Equivalent parameter of primer DNA concentration for the internal oligo.</p></body></html></string> 1971 </property> 1972 <property name="maximum"> 1973 <double>9999.989999999999782</double> 1974 </property> 1975 </widget> 1976 </item> 1977 </layout> 1978 </item> 1979 <item> 1980 <spacer name="verticalSpacer_3"> 1981 <property name="orientation"> 1982 <enum>Qt::Vertical</enum> 1983 </property> 1984 <property name="sizeHint" stdset="0"> 1985 <size> 1986 <width>20</width> 1987 <height>40</height> 1988 </size> 1989 </property> 1990 </spacer> 1991 </item> 1992 </layout> 1993 </widget> 1994 <widget class="QWidget" name="tab_PenaltyWeights"> 1995 <attribute name="title"> 1996 <string>Penalty Weights</string> 1997 </attribute> 1998 <attribute name="toolTip"> 1999 <string><html><head/><body><p>This section describes &quot;penalty weights&quot;, which allow the user to modify the criteria that Primer3 uses to select the &quot;best&quot; primers.</p><p>There are two classes of weights: for some parameters there is a 'Lt' (less than) and a 'Gt' (greater than) weight. These are the weights that Primer3 uses when the value is less or greater than (respectively) the specified optimum.</p></body></html></string> 2000 </attribute> 2001 <layout class="QHBoxLayout" name="horizontalLayout_3"> 2002 <item> 2003 <layout class="QVBoxLayout" name="verticalLayout_5"> 2004 <item> 2005 <widget class="QLabel" name="label_55"> 2006 <property name="font"> 2007 <font> 2008 <weight>75</weight> 2009 <bold>true</bold> 2010 </font> 2011 </property> 2012 <property name="text"> 2013 <string>Primers</string> 2014 </property> 2015 </widget> 2016 </item> 2017 <item> 2018 <layout class="QGridLayout" name="gridLayout_5"> 2019 <item row="0" column="0"> 2020 <widget class="QLabel" name="label_6"> 2021 <property name="text"> 2022 <string>Tm</string> 2023 </property> 2024 </widget> 2025 </item> 2026 <item row="1" column="0"> 2027 <widget class="QLabel" name="label_7"> 2028 <property name="text"> 2029 <string>Size </string> 2030 </property> 2031 </widget> 2032 </item> 2033 <item row="2" column="0"> 2034 <widget class="QLabel" name="label_8"> 2035 <property name="text"> 2036 <string>GC%</string> 2037 </property> 2038 </widget> 2039 </item> 2040 <item row="0" column="1"> 2041 <widget class="QLabel" name="label_11"> 2042 <property name="text"> 2043 <string>Lt:</string> 2044 </property> 2045 </widget> 2046 </item> 2047 <item row="1" column="1"> 2048 <widget class="QLabel" name="label_12"> 2049 <property name="text"> 2050 <string>Lt:</string> 2051 </property> 2052 </widget> 2053 </item> 2054 <item row="2" column="1"> 2055 <widget class="QLabel" name="label_13"> 2056 <property name="text"> 2057 <string>Lt:</string> 2058 </property> 2059 </widget> 2060 </item> 2061 <item row="0" column="2"> 2062 <widget class="QDoubleSpinBox" name="edit_PRIMER_WT_TM_LT"> 2063 <property name="sizePolicy"> 2064 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 2065 <horstretch>0</horstretch> 2066 <verstretch>0</verstretch> 2067 </sizepolicy> 2068 </property> 2069 <property name="toolTip"> 2070 <string><html><head/><body><p>Penalty weight for corressponding parameter of a primer less than (Lt) or greater than (Gt) the optimal value.</p></body></html></string> 2071 </property> 2072 <property name="maximum"> 2073 <double>9999.989999999999782</double> 2074 </property> 2075 </widget> 2076 </item> 2077 <item row="1" column="2"> 2078 <widget class="QDoubleSpinBox" name="edit_PRIMER_WT_SIZE_LT"> 2079 <property name="sizePolicy"> 2080 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 2081 <horstretch>0</horstretch> 2082 <verstretch>0</verstretch> 2083 </sizepolicy> 2084 </property> 2085 <property name="toolTip"> 2086 <string><html><head/><body><p>Penalty weight for corressponding parameter of a primer less than (Lt) or greater than (Gt) the optimal value.</p></body></html></string> 2087 </property> 2088 <property name="maximum"> 2089 <double>9999.989999999999782</double> 2090 </property> 2091 </widget> 2092 </item> 2093 <item row="2" column="2"> 2094 <widget class="QDoubleSpinBox" name="edit_PRIMER_WT_GC_PERCENT_LT"> 2095 <property name="sizePolicy"> 2096 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 2097 <horstretch>0</horstretch> 2098 <verstretch>0</verstretch> 2099 </sizepolicy> 2100 </property> 2101 <property name="toolTip"> 2102 <string><html><head/><body><p>Penalty weight for corressponding parameter of a primer less than (Lt) or greater than (Gt) the optimal value.</p></body></html></string> 2103 </property> 2104 <property name="maximum"> 2105 <double>9999.989999999999782</double> 2106 </property> 2107 </widget> 2108 </item> 2109 <item row="0" column="3"> 2110 <widget class="QLabel" name="label_14"> 2111 <property name="text"> 2112 <string>Gt:</string> 2113 </property> 2114 </widget> 2115 </item> 2116 <item row="1" column="3"> 2117 <widget class="QLabel" name="label_15"> 2118 <property name="text"> 2119 <string>Gt:</string> 2120 </property> 2121 </widget> 2122 </item> 2123 <item row="2" column="3"> 2124 <widget class="QLabel" name="label_16"> 2125 <property name="text"> 2126 <string>Gt:</string> 2127 </property> 2128 </widget> 2129 </item> 2130 <item row="0" column="4"> 2131 <widget class="QDoubleSpinBox" name="edit_PRIMER_WT_TM_GT"> 2132 <property name="sizePolicy"> 2133 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 2134 <horstretch>0</horstretch> 2135 <verstretch>0</verstretch> 2136 </sizepolicy> 2137 </property> 2138 <property name="toolTip"> 2139 <string><html><head/><body><p>Penalty weight for corressponding parameter of a primer less than (Lt) or greater than (Gt) the optimal value.</p></body></html></string> 2140 </property> 2141 <property name="maximum"> 2142 <double>9999.989999999999782</double> 2143 </property> 2144 </widget> 2145 </item> 2146 <item row="1" column="4"> 2147 <widget class="QDoubleSpinBox" name="edit_PRIMER_WT_SIZE_GT"> 2148 <property name="sizePolicy"> 2149 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 2150 <horstretch>0</horstretch> 2151 <verstretch>0</verstretch> 2152 </sizepolicy> 2153 </property> 2154 <property name="toolTip"> 2155 <string><html><head/><body><p>Penalty weight for corressponding parameter of a primer less than (Lt) or greater than (Gt) the optimal value.</p></body></html></string> 2156 </property> 2157 <property name="maximum"> 2158 <double>9999.989999999999782</double> 2159 </property> 2160 </widget> 2161 </item> 2162 <item row="2" column="4"> 2163 <widget class="QDoubleSpinBox" name="edit_PRIMER_WT_GC_PERCENT_GT"> 2164 <property name="sizePolicy"> 2165 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 2166 <horstretch>0</horstretch> 2167 <verstretch>0</verstretch> 2168 </sizepolicy> 2169 </property> 2170 <property name="toolTip"> 2171 <string><html><head/><body><p>Penalty weight for corressponding parameter of a primer less than (Lt) or greater than (Gt) the optimal value.</p></body></html></string> 2172 </property> 2173 <property name="maximum"> 2174 <double>9999.989999999999782</double> 2175 </property> 2176 </widget> 2177 </item> 2178 </layout> 2179 </item> 2180 <item> 2181 <widget class="Line" name="line_11"> 2182 <property name="orientation"> 2183 <enum>Qt::Horizontal</enum> 2184 </property> 2185 </widget> 2186 </item> 2187 <item> 2188 <layout class="QGridLayout" name="gridLayout_6"> 2189 <item row="0" column="0"> 2190 <widget class="QLabel" name="label_17"> 2191 <property name="text"> 2192 <string>Self complementarity</string> 2193 </property> 2194 </widget> 2195 </item> 2196 <item row="1" column="0"> 2197 <widget class="QLabel" name="label_18"> 2198 <property name="text"> 2199 <string>3' self complementarity</string> 2200 </property> 2201 </widget> 2202 </item> 2203 <item row="2" column="0"> 2204 <widget class="QLabel" name="label_19"> 2205 <property name="text"> 2206 <string>#N's</string> 2207 </property> 2208 </widget> 2209 </item> 2210 <item row="3" column="0"> 2211 <widget class="QLabel" name="label_20"> 2212 <property name="text"> 2213 <string>Mispriming</string> 2214 </property> 2215 </widget> 2216 </item> 2217 <item row="4" column="0"> 2218 <widget class="QLabel" name="label_21"> 2219 <property name="text"> 2220 <string>Sequence quality</string> 2221 </property> 2222 </widget> 2223 </item> 2224 <item row="5" column="0"> 2225 <widget class="QLabel" name="label_22"> 2226 <property name="text"> 2227 <string>End sequence quality</string> 2228 </property> 2229 </widget> 2230 </item> 2231 <item row="6" column="0"> 2232 <widget class="QLabel" name="label_23"> 2233 <property name="text"> 2234 <string>Position penalty</string> 2235 </property> 2236 </widget> 2237 </item> 2238 <item row="7" column="0"> 2239 <widget class="QLabel" name="label_24"> 2240 <property name="text"> 2241 <string>End stability</string> 2242 </property> 2243 </widget> 2244 </item> 2245 <item row="8" column="0"> 2246 <widget class="QLabel" name="label_25"> 2247 <property name="text"> 2248 <string>Template mispriming</string> 2249 </property> 2250 </widget> 2251 </item> 2252 <item row="0" column="1"> 2253 <widget class="QDoubleSpinBox" name="edit_PRIMER_WT_COMPL_ANY"> 2254 <property name="sizePolicy"> 2255 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 2256 <horstretch>0</horstretch> 2257 <verstretch>0</verstretch> 2258 </sizepolicy> 2259 </property> 2260 <property name="toolTip"> 2261 <string><html><head/><body><p>Penalty weight for a primer parameter different from predefined optimum value.</p></body></html></string> 2262 </property> 2263 <property name="maximum"> 2264 <double>9999.989999999999782</double> 2265 </property> 2266 </widget> 2267 </item> 2268 <item row="1" column="1"> 2269 <widget class="QDoubleSpinBox" name="edit_PRIMER_WT_COMPL_END"> 2270 <property name="sizePolicy"> 2271 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 2272 <horstretch>0</horstretch> 2273 <verstretch>0</verstretch> 2274 </sizepolicy> 2275 </property> 2276 <property name="toolTip"> 2277 <string><html><head/><body><p>Penalty weight for a primer parameter different from predefined optimum value.</p></body></html></string> 2278 </property> 2279 <property name="maximum"> 2280 <double>9999.989999999999782</double> 2281 </property> 2282 </widget> 2283 </item> 2284 <item row="2" column="1"> 2285 <widget class="QDoubleSpinBox" name="edit_PRIMER_WT_NUM_NS"> 2286 <property name="sizePolicy"> 2287 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 2288 <horstretch>0</horstretch> 2289 <verstretch>0</verstretch> 2290 </sizepolicy> 2291 </property> 2292 <property name="toolTip"> 2293 <string><html><head/><body><p>Penalty weight for a primer parameter different from predefined optimum value.</p></body></html></string> 2294 </property> 2295 <property name="maximum"> 2296 <double>9999.989999999999782</double> 2297 </property> 2298 </widget> 2299 </item> 2300 <item row="3" column="1"> 2301 <widget class="QDoubleSpinBox" name="edit_PRIMER_WT_REP_SIM"> 2302 <property name="sizePolicy"> 2303 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 2304 <horstretch>0</horstretch> 2305 <verstretch>0</verstretch> 2306 </sizepolicy> 2307 </property> 2308 <property name="toolTip"> 2309 <string><html><head/><body><p>Penalty weight for a primer parameter different from predefined optimum value.</p></body></html></string> 2310 </property> 2311 <property name="maximum"> 2312 <double>9999.989999999999782</double> 2313 </property> 2314 </widget> 2315 </item> 2316 <item row="4" column="1"> 2317 <widget class="QDoubleSpinBox" name="edit_PRIMER_WT_SEQ_QUAL"> 2318 <property name="sizePolicy"> 2319 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 2320 <horstretch>0</horstretch> 2321 <verstretch>0</verstretch> 2322 </sizepolicy> 2323 </property> 2324 <property name="toolTip"> 2325 <string><html><head/><body><p>Penalty weight for a primer parameter different from predefined optimum value.</p></body></html></string> 2326 </property> 2327 <property name="maximum"> 2328 <double>9999.989999999999782</double> 2329 </property> 2330 </widget> 2331 </item> 2332 <item row="5" column="1"> 2333 <widget class="QDoubleSpinBox" name="edit_PRIMER_WT_END_QUAL"> 2334 <property name="sizePolicy"> 2335 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 2336 <horstretch>0</horstretch> 2337 <verstretch>0</verstretch> 2338 </sizepolicy> 2339 </property> 2340 <property name="toolTip"> 2341 <string><html><head/><body><p>Penalty weight for a primer parameter different from predefined optimum value.</p></body></html></string> 2342 </property> 2343 <property name="maximum"> 2344 <double>9999.989999999999782</double> 2345 </property> 2346 </widget> 2347 </item> 2348 <item row="6" column="1"> 2349 <widget class="QDoubleSpinBox" name="edit_PRIMER_WT_POS_PENALTY"> 2350 <property name="sizePolicy"> 2351 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 2352 <horstretch>0</horstretch> 2353 <verstretch>0</verstretch> 2354 </sizepolicy> 2355 </property> 2356 <property name="toolTip"> 2357 <string><html><head/><body><p>Determines the overall weight of the position penalty in calculating the penalty for a primer.</p></body></html></string> 2358 </property> 2359 <property name="maximum"> 2360 <double>9999.989999999999782</double> 2361 </property> 2362 </widget> 2363 </item> 2364 <item row="7" column="1"> 2365 <widget class="QDoubleSpinBox" name="edit_PRIMER_WT_END_STABILITY"> 2366 <property name="sizePolicy"> 2367 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 2368 <horstretch>0</horstretch> 2369 <verstretch>0</verstretch> 2370 </sizepolicy> 2371 </property> 2372 <property name="toolTip"> 2373 <string><html><head/><body><p>Penalty weight for a primer parameter different from predefined optimum value.</p></body></html></string> 2374 </property> 2375 <property name="maximum"> 2376 <double>9999.989999999999782</double> 2377 </property> 2378 </widget> 2379 </item> 2380 <item row="8" column="1"> 2381 <widget class="QDoubleSpinBox" name="edit_PRIMER_WT_TEMPLATE_MISPRIMING"> 2382 <property name="sizePolicy"> 2383 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 2384 <horstretch>0</horstretch> 2385 <verstretch>0</verstretch> 2386 </sizepolicy> 2387 </property> 2388 <property name="toolTip"> 2389 <string><html><head/><body><p>Penalty weight for a primer parameter different from predefined optimum value.</p></body></html></string> 2390 </property> 2391 <property name="maximum"> 2392 <double>9999.989999999999782</double> 2393 </property> 2394 </widget> 2395 </item> 2396 </layout> 2397 </item> 2398 <item> 2399 <spacer name="verticalSpacer_4"> 2400 <property name="orientation"> 2401 <enum>Qt::Vertical</enum> 2402 </property> 2403 <property name="sizeHint" stdset="0"> 2404 <size> 2405 <width>20</width> 2406 <height>40</height> 2407 </size> 2408 </property> 2409 </spacer> 2410 </item> 2411 </layout> 2412 </item> 2413 <item> 2414 <widget class="Line" name="line_7"> 2415 <property name="orientation"> 2416 <enum>Qt::Vertical</enum> 2417 </property> 2418 </widget> 2419 </item> 2420 <item> 2421 <layout class="QVBoxLayout" name="verticalLayout_3"> 2422 <item> 2423 <widget class="QLabel" name="label_56"> 2424 <property name="font"> 2425 <font> 2426 <weight>75</weight> 2427 <bold>true</bold> 2428 </font> 2429 </property> 2430 <property name="text"> 2431 <string>Primer Pairs</string> 2432 </property> 2433 </widget> 2434 </item> 2435 <item> 2436 <layout class="QGridLayout" name="gridLayout_9"> 2437 <item row="0" column="0"> 2438 <widget class="QLabel" name="label_26"> 2439 <property name="text"> 2440 <string>Product size</string> 2441 </property> 2442 </widget> 2443 </item> 2444 <item row="1" column="0"> 2445 <widget class="QLabel" name="label_28"> 2446 <property name="text"> 2447 <string>Product Tm</string> 2448 </property> 2449 </widget> 2450 </item> 2451 <item row="0" column="2"> 2452 <widget class="QDoubleSpinBox" name="edit_PRIMER_PAIR_WT_PRODUCT_SIZE_LT"> 2453 <property name="sizePolicy"> 2454 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 2455 <horstretch>0</horstretch> 2456 <verstretch>0</verstretch> 2457 </sizepolicy> 2458 </property> 2459 <property name="toolTip"> 2460 <string><html><head/><body><p>Penalty weight for corressponding parameter of a primer pair less than (Lt) or greater than (Gt) the optimal value.</p></body></html></string> 2461 </property> 2462 <property name="maximum"> 2463 <double>9999.989999999999782</double> 2464 </property> 2465 </widget> 2466 </item> 2467 <item row="1" column="2"> 2468 <widget class="QDoubleSpinBox" name="edit_PRIMER_PAIR_WT_PRODUCT_TM_LT"> 2469 <property name="sizePolicy"> 2470 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 2471 <horstretch>0</horstretch> 2472 <verstretch>0</verstretch> 2473 </sizepolicy> 2474 </property> 2475 <property name="toolTip"> 2476 <string><html><head/><body><p>Penalty weight for corressponding parameter of a primer pair less than (Lt) or greater than (Gt) the optimal value.</p></body></html></string> 2477 </property> 2478 <property name="maximum"> 2479 <double>9999.989999999999782</double> 2480 </property> 2481 </widget> 2482 </item> 2483 <item row="0" column="1"> 2484 <widget class="QLabel" name="label_45"> 2485 <property name="text"> 2486 <string>Lt:</string> 2487 </property> 2488 </widget> 2489 </item> 2490 <item row="1" column="1"> 2491 <widget class="QLabel" name="label_46"> 2492 <property name="text"> 2493 <string>Lt:</string> 2494 </property> 2495 </widget> 2496 </item> 2497 <item row="0" column="3"> 2498 <widget class="QLabel" name="label_47"> 2499 <property name="text"> 2500 <string>Gt:</string> 2501 </property> 2502 </widget> 2503 </item> 2504 <item row="1" column="3"> 2505 <widget class="QLabel" name="label_48"> 2506 <property name="text"> 2507 <string>Gt:</string> 2508 </property> 2509 </widget> 2510 </item> 2511 <item row="0" column="4"> 2512 <widget class="QDoubleSpinBox" name="edit_PRIMER_PAIR_WT_PRODUCT_SIZE_GT"> 2513 <property name="sizePolicy"> 2514 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 2515 <horstretch>0</horstretch> 2516 <verstretch>0</verstretch> 2517 </sizepolicy> 2518 </property> 2519 <property name="toolTip"> 2520 <string><html><head/><body><p>Penalty weight for corressponding parameter of a primer pair less than (Lt) or greater than (Gt) the optimal value.</p></body></html></string> 2521 </property> 2522 <property name="maximum"> 2523 <double>9999.989999999999782</double> 2524 </property> 2525 </widget> 2526 </item> 2527 <item row="1" column="4"> 2528 <widget class="QDoubleSpinBox" name="edit_PRIMER_PAIR_WT_PRODUCT_TM_GT"> 2529 <property name="sizePolicy"> 2530 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 2531 <horstretch>0</horstretch> 2532 <verstretch>0</verstretch> 2533 </sizepolicy> 2534 </property> 2535 <property name="toolTip"> 2536 <string><html><head/><body><p>Penalty weight for corressponding parameter of a primer pair less than (Lt) or greater than (Gt) the optimal value.</p></body></html></string> 2537 </property> 2538 <property name="maximum"> 2539 <double>9999.989999999999782</double> 2540 </property> 2541 </widget> 2542 </item> 2543 </layout> 2544 </item> 2545 <item> 2546 <widget class="Line" name="line_12"> 2547 <property name="orientation"> 2548 <enum>Qt::Horizontal</enum> 2549 </property> 2550 </widget> 2551 </item> 2552 <item> 2553 <layout class="QGridLayout" name="gridLayout_10"> 2554 <item row="0" column="0"> 2555 <widget class="QLabel" name="label_27"> 2556 <property name="text"> 2557 <string>Tm difference</string> 2558 </property> 2559 </widget> 2560 </item> 2561 <item row="1" column="0"> 2562 <widget class="QLabel" name="label_29"> 2563 <property name="text"> 2564 <string>Any complementarity</string> 2565 </property> 2566 </widget> 2567 </item> 2568 <item row="2" column="0"> 2569 <widget class="QLabel" name="label_30"> 2570 <property name="text"> 2571 <string>3' complementarity</string> 2572 </property> 2573 </widget> 2574 </item> 2575 <item row="3" column="0"> 2576 <widget class="QLabel" name="label_31"> 2577 <property name="text"> 2578 <string>Pair mispriming</string> 2579 </property> 2580 </widget> 2581 </item> 2582 <item row="4" column="0"> 2583 <widget class="QLabel" name="label_32"> 2584 <property name="text"> 2585 <string>Primer penalty weight</string> 2586 </property> 2587 </widget> 2588 </item> 2589 <item row="5" column="0"> 2590 <widget class="QLabel" name="label_33"> 2591 <property name="text"> 2592 <string>Hyb oligo penalty weight</string> 2593 </property> 2594 </widget> 2595 </item> 2596 <item row="6" column="0"> 2597 <widget class="QLabel" name="label_37"> 2598 <property name="text"> 2599 <string>Primer pair template mispriming weight</string> 2600 </property> 2601 </widget> 2602 </item> 2603 <item row="0" column="1"> 2604 <widget class="QDoubleSpinBox" name="edit_PRIMER_PAIR_WT_DIFF_TM"> 2605 <property name="sizePolicy"> 2606 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 2607 <horstretch>0</horstretch> 2608 <verstretch>0</verstretch> 2609 </sizepolicy> 2610 </property> 2611 <property name="toolTip"> 2612 <string><html><head/><body><p>Penalty weight for a primer pair parameter different from predefined optimum value.</p></body></html></string> 2613 </property> 2614 <property name="maximum"> 2615 <double>9999.989999999999782</double> 2616 </property> 2617 </widget> 2618 </item> 2619 <item row="1" column="1"> 2620 <widget class="QDoubleSpinBox" name="edit_PRIMER_PAIR_WT_COMPL_ANY"> 2621 <property name="sizePolicy"> 2622 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 2623 <horstretch>0</horstretch> 2624 <verstretch>0</verstretch> 2625 </sizepolicy> 2626 </property> 2627 <property name="toolTip"> 2628 <string><html><head/><body><p>Penalty weight for a primer pair parameter different from predefined optimum value.</p></body></html></string> 2629 </property> 2630 <property name="maximum"> 2631 <double>9999.989999999999782</double> 2632 </property> 2633 </widget> 2634 </item> 2635 <item row="2" column="1"> 2636 <widget class="QDoubleSpinBox" name="edit_PRIMER_PAIR_WT_COMPL_END"> 2637 <property name="sizePolicy"> 2638 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 2639 <horstretch>0</horstretch> 2640 <verstretch>0</verstretch> 2641 </sizepolicy> 2642 </property> 2643 <property name="toolTip"> 2644 <string><html><head/><body><p>Penalty weight for a primer pair parameter different from predefined optimum value.</p></body></html></string> 2645 </property> 2646 <property name="maximum"> 2647 <double>9999.989999999999782</double> 2648 </property> 2649 </widget> 2650 </item> 2651 <item row="3" column="1"> 2652 <widget class="QDoubleSpinBox" name="edit_PRIMER_PAIR_WT_REP_SIM"> 2653 <property name="sizePolicy"> 2654 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 2655 <horstretch>0</horstretch> 2656 <verstretch>0</verstretch> 2657 </sizepolicy> 2658 </property> 2659 <property name="toolTip"> 2660 <string><html><head/><body><p>Penalty weight for a primer pair parameter different from predefined optimum value.</p></body></html></string> 2661 </property> 2662 <property name="maximum"> 2663 <double>9999.989999999999782</double> 2664 </property> 2665 </widget> 2666 </item> 2667 <item row="4" column="1"> 2668 <widget class="QDoubleSpinBox" name="edit_PRIMER_PAIR_WT_PR_PENALTY"> 2669 <property name="sizePolicy"> 2670 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 2671 <horstretch>0</horstretch> 2672 <verstretch>0</verstretch> 2673 </sizepolicy> 2674 </property> 2675 <property name="toolTip"> 2676 <string><html><head/><body><p>Penalty weight for a primer pair parameter different from predefined optimum value.</p></body></html></string> 2677 </property> 2678 <property name="maximum"> 2679 <double>9999.989999999999782</double> 2680 </property> 2681 </widget> 2682 </item> 2683 <item row="5" column="1"> 2684 <widget class="QDoubleSpinBox" name="edit_PRIMER_PAIR_WT_IO_PENALTY"> 2685 <property name="sizePolicy"> 2686 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 2687 <horstretch>0</horstretch> 2688 <verstretch>0</verstretch> 2689 </sizepolicy> 2690 </property> 2691 <property name="toolTip"> 2692 <string><html><head/><body><p>Penalty weight for a primer pair parameter different from predefined optimum value.</p></body></html></string> 2693 </property> 2694 <property name="maximum"> 2695 <double>9999.989999999999782</double> 2696 </property> 2697 </widget> 2698 </item> 2699 <item row="6" column="1"> 2700 <widget class="QDoubleSpinBox" name="edit_PRIMER_PAIR_WT_TEMPLATE_MISPRIMING"> 2701 <property name="sizePolicy"> 2702 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 2703 <horstretch>0</horstretch> 2704 <verstretch>0</verstretch> 2705 </sizepolicy> 2706 </property> 2707 <property name="toolTip"> 2708 <string><html><head/><body><p>Penalty weight for a primer pair parameter different from predefined optimum value.</p></body></html></string> 2709 </property> 2710 <property name="maximum"> 2711 <double>9999.989999999999782</double> 2712 </property> 2713 </widget> 2714 </item> 2715 </layout> 2716 </item> 2717 <item> 2718 <spacer name="verticalSpacer_5"> 2719 <property name="orientation"> 2720 <enum>Qt::Vertical</enum> 2721 </property> 2722 <property name="sizeHint" stdset="0"> 2723 <size> 2724 <width>20</width> 2725 <height>40</height> 2726 </size> 2727 </property> 2728 </spacer> 2729 </item> 2730 </layout> 2731 </item> 2732 <item> 2733 <widget class="Line" name="line_8"> 2734 <property name="orientation"> 2735 <enum>Qt::Vertical</enum> 2736 </property> 2737 </widget> 2738 </item> 2739 <item> 2740 <layout class="QVBoxLayout" name="verticalLayout_6"> 2741 <item> 2742 <widget class="QLabel" name="label_57"> 2743 <property name="font"> 2744 <font> 2745 <weight>75</weight> 2746 <bold>true</bold> 2747 </font> 2748 </property> 2749 <property name="text"> 2750 <string>Hyb Oligos</string> 2751 </property> 2752 </widget> 2753 </item> 2754 <item> 2755 <layout class="QGridLayout" name="gridLayout_11"> 2756 <item row="0" column="0"> 2757 <widget class="QLabel" name="label_38"> 2758 <property name="text"> 2759 <string>Hyb oligo Tm</string> 2760 </property> 2761 </widget> 2762 </item> 2763 <item row="1" column="0"> 2764 <widget class="QLabel" name="label_40"> 2765 <property name="text"> 2766 <string>Hyb oligo size</string> 2767 </property> 2768 </widget> 2769 </item> 2770 <item row="2" column="0"> 2771 <widget class="QLabel" name="label_41"> 2772 <property name="text"> 2773 <string>Hyb oligo GC%</string> 2774 </property> 2775 </widget> 2776 </item> 2777 <item row="0" column="1"> 2778 <widget class="QLabel" name="label_49"> 2779 <property name="text"> 2780 <string>Lt:</string> 2781 </property> 2782 </widget> 2783 </item> 2784 <item row="1" column="1"> 2785 <widget class="QLabel" name="label_50"> 2786 <property name="text"> 2787 <string>Lt:</string> 2788 </property> 2789 </widget> 2790 </item> 2791 <item row="2" column="1"> 2792 <widget class="QLabel" name="label_51"> 2793 <property name="text"> 2794 <string>Lt:</string> 2795 </property> 2796 </widget> 2797 </item> 2798 <item row="0" column="2"> 2799 <widget class="QDoubleSpinBox" name="edit_PRIMER_IO_WT_TM_LT"> 2800 <property name="sizePolicy"> 2801 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 2802 <horstretch>0</horstretch> 2803 <verstretch>0</verstretch> 2804 </sizepolicy> 2805 </property> 2806 <property name="toolTip"> 2807 <string><html><head/><body><p>Penalty weight for corressponding parameter of a internal oligo less than (Lt) or greater than (Gt) the optimal value.</p></body></html></string> 2808 </property> 2809 <property name="maximum"> 2810 <double>9999.989999999999782</double> 2811 </property> 2812 </widget> 2813 </item> 2814 <item row="1" column="2"> 2815 <widget class="QDoubleSpinBox" name="edit_PRIMER_IO_WT_SIZE_LT"> 2816 <property name="sizePolicy"> 2817 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 2818 <horstretch>0</horstretch> 2819 <verstretch>0</verstretch> 2820 </sizepolicy> 2821 </property> 2822 <property name="toolTip"> 2823 <string><html><head/><body><p>Penalty weight for corressponding parameter of a internal oligo less than (Lt) or greater than (Gt) the optimal value.</p></body></html></string> 2824 </property> 2825 <property name="maximum"> 2826 <double>9999.989999999999782</double> 2827 </property> 2828 </widget> 2829 </item> 2830 <item row="2" column="2"> 2831 <widget class="QDoubleSpinBox" name="edit_PRIMER_IO_WT_GC_PERCENT_LT"> 2832 <property name="sizePolicy"> 2833 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 2834 <horstretch>0</horstretch> 2835 <verstretch>0</verstretch> 2836 </sizepolicy> 2837 </property> 2838 <property name="toolTip"> 2839 <string><html><head/><body><p>Penalty weight for corressponding parameter of a internal oligo less than (Lt) or greater than (Gt) the optimal value.</p></body></html></string> 2840 </property> 2841 <property name="maximum"> 2842 <double>9999.989999999999782</double> 2843 </property> 2844 </widget> 2845 </item> 2846 <item row="0" column="3"> 2847 <widget class="QLabel" name="label_52"> 2848 <property name="text"> 2849 <string>Gt:</string> 2850 </property> 2851 </widget> 2852 </item> 2853 <item row="1" column="3"> 2854 <widget class="QLabel" name="label_53"> 2855 <property name="text"> 2856 <string>Gt:</string> 2857 </property> 2858 </widget> 2859 </item> 2860 <item row="2" column="3"> 2861 <widget class="QLabel" name="label_54"> 2862 <property name="text"> 2863 <string>Gt:</string> 2864 </property> 2865 </widget> 2866 </item> 2867 <item row="0" column="4"> 2868 <widget class="QDoubleSpinBox" name="edit_PRIMER_IO_WT_TM_GT"> 2869 <property name="sizePolicy"> 2870 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 2871 <horstretch>0</horstretch> 2872 <verstretch>0</verstretch> 2873 </sizepolicy> 2874 </property> 2875 <property name="toolTip"> 2876 <string><html><head/><body><p>Penalty weight for corressponding parameter of a internal oligo less than (Lt) or greater than (Gt) the optimal value.</p></body></html></string> 2877 </property> 2878 <property name="maximum"> 2879 <double>9999.989999999999782</double> 2880 </property> 2881 </widget> 2882 </item> 2883 <item row="1" column="4"> 2884 <widget class="QDoubleSpinBox" name="edit_PRIMER_IO_WT_SIZE_GT"> 2885 <property name="sizePolicy"> 2886 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 2887 <horstretch>0</horstretch> 2888 <verstretch>0</verstretch> 2889 </sizepolicy> 2890 </property> 2891 <property name="toolTip"> 2892 <string><html><head/><body><p>Penalty weight for corressponding parameter of a internal oligo less than (Lt) or greater than (Gt) the optimal value.</p></body></html></string> 2893 </property> 2894 <property name="maximum"> 2895 <double>9999.989999999999782</double> 2896 </property> 2897 </widget> 2898 </item> 2899 <item row="2" column="4"> 2900 <widget class="QDoubleSpinBox" name="edit_PRIMER_IO_WT_GC_PERCENT_GT"> 2901 <property name="sizePolicy"> 2902 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 2903 <horstretch>0</horstretch> 2904 <verstretch>0</verstretch> 2905 </sizepolicy> 2906 </property> 2907 <property name="toolTip"> 2908 <string><html><head/><body><p>Penalty weight for corressponding parameter of a internal oligo less than (Lt) or greater than (Gt) the optimal value.</p></body></html></string> 2909 </property> 2910 <property name="maximum"> 2911 <double>9999.989999999999782</double> 2912 </property> 2913 </widget> 2914 </item> 2915 </layout> 2916 </item> 2917 <item> 2918 <widget class="Line" name="line_13"> 2919 <property name="orientation"> 2920 <enum>Qt::Horizontal</enum> 2921 </property> 2922 </widget> 2923 </item> 2924 <item> 2925 <layout class="QGridLayout" name="gridLayout_12"> 2926 <item row="0" column="0"> 2927 <widget class="QLabel" name="label_39"> 2928 <property name="text"> 2929 <string>Hyb oligo self complementarity</string> 2930 </property> 2931 </widget> 2932 </item> 2933 <item row="1" column="0"> 2934 <widget class="QLabel" name="label_42"> 2935 <property name="text"> 2936 <string>Hyb oligo #N's</string> 2937 </property> 2938 </widget> 2939 </item> 2940 <item row="2" column="0"> 2941 <widget class="QLabel" name="label_43"> 2942 <property name="text"> 2943 <string>Hyb oligo mishybing</string> 2944 </property> 2945 </widget> 2946 </item> 2947 <item row="3" column="0"> 2948 <widget class="QLabel" name="label_44"> 2949 <property name="text"> 2950 <string>Hyb oligo sequence quality</string> 2951 </property> 2952 </widget> 2953 </item> 2954 <item row="0" column="1"> 2955 <widget class="QDoubleSpinBox" name="edit_PRIMER_IO_WT_COMPL_ANY"> 2956 <property name="sizePolicy"> 2957 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 2958 <horstretch>0</horstretch> 2959 <verstretch>0</verstretch> 2960 </sizepolicy> 2961 </property> 2962 <property name="toolTip"> 2963 <string><html><head/><body><p>Penalty weight for an internal oligo parameter different from predefined optimum value.</p></body></html></string> 2964 </property> 2965 <property name="maximum"> 2966 <double>9999.989999999999782</double> 2967 </property> 2968 </widget> 2969 </item> 2970 <item row="1" column="1"> 2971 <widget class="QDoubleSpinBox" name="edit_PRIMER_IO_WT_NUM_NS"> 2972 <property name="sizePolicy"> 2973 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 2974 <horstretch>0</horstretch> 2975 <verstretch>0</verstretch> 2976 </sizepolicy> 2977 </property> 2978 <property name="toolTip"> 2979 <string><html><head/><body><p>Penalty weight for an internal oligo parameter different from predefined optimum value.</p></body></html></string> 2980 </property> 2981 <property name="maximum"> 2982 <double>9999.989999999999782</double> 2983 </property> 2984 </widget> 2985 </item> 2986 <item row="2" column="1"> 2987 <widget class="QDoubleSpinBox" name="edit_PRIMER_IO_WT_REP_SIM"> 2988 <property name="sizePolicy"> 2989 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 2990 <horstretch>0</horstretch> 2991 <verstretch>0</verstretch> 2992 </sizepolicy> 2993 </property> 2994 <property name="toolTip"> 2995 <string><html><head/><body><p>Penalty weight for an internal oligo parameter different from predefined optimum value.</p></body></html></string> 2996 </property> 2997 <property name="maximum"> 2998 <double>9999.989999999999782</double> 2999 </property> 3000 </widget> 3001 </item> 3002 <item row="3" column="1"> 3003 <widget class="QDoubleSpinBox" name="edit_PRIMER_IO_WT_SEQ_QUAL"> 3004 <property name="sizePolicy"> 3005 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 3006 <horstretch>0</horstretch> 3007 <verstretch>0</verstretch> 3008 </sizepolicy> 3009 </property> 3010 <property name="toolTip"> 3011 <string><html><head/><body><p>Penalty weight for an internal oligo parameter different from predefined optimum value.</p></body></html></string> 3012 </property> 3013 <property name="maximum"> 3014 <double>9999.989999999999782</double> 3015 </property> 3016 </widget> 3017 </item> 3018 </layout> 3019 </item> 3020 <item> 3021 <spacer name="verticalSpacer_6"> 3022 <property name="orientation"> 3023 <enum>Qt::Vertical</enum> 3024 </property> 3025 <property name="sizeHint" stdset="0"> 3026 <size> 3027 <width>20</width> 3028 <height>40</height> 3029 </size> 3030 </property> 3031 </spacer> 3032 </item> 3033 </layout> 3034 </item> 3035 </layout> 3036 </widget> 3037 <widget class="QWidget" name="tab_spanIntronExon"> 3038 <attribute name="title"> 3039 <string>RT-PCR</string> 3040 </attribute> 3041 <attribute name="toolTip"> 3042 <string><html><head/><body><p>In this section user can specify if primer product must overlap exon-exon junction or span intron. This only applies when designing primers for a cDNA (mRNA) sequence with annotated exons.</p></body></html></string> 3043 </attribute> 3044 <layout class="QVBoxLayout" name="verticalLayout_9"> 3045 <item> 3046 <widget class="QGroupBox" name="spanIntronExonBox"> 3047 <property name="toolTip"> 3048 <string><html><head/><body><p>This feature allows to specify if primer product must span intron-exon boundaries.</p><p>Checking this option will result in ignoring <span style=" font-style:italic;">Excluded</span> and <span style=" font-style:italic;">Target Regions</span> from Main section.</p></body></html></string> 3049 </property> 3050 <property name="title"> 3051 <string>Design primers for RT-PCR analysis</string> 3052 </property> 3053 <property name="checkable"> 3054 <bool>true</bool> 3055 </property> 3056 <property name="checked"> 3057 <bool>false</bool> 3058 </property> 3059 <layout class="QVBoxLayout" name="verticalLayout_8"> 3060 <item> 3061 <widget class="QGroupBox" name="groupBox_3"> 3062 <property name="title"> 3063 <string>mRNA sequence</string> 3064 </property> 3065 <layout class="QVBoxLayout" name="verticalLayout_10"> 3066 <item> 3067 <layout class="QHBoxLayout" name="horizontalLayout_5"> 3068 <item> 3069 <widget class="QLabel" name="label_9"> 3070 <property name="text"> 3071 <string>Exon annotation name:</string> 3072 </property> 3073 </widget> 3074 </item> 3075 <item> 3076 <widget class="QLineEdit" name="exonNameEdit"> 3077 <property name="toolTip"> 3078 <string><html><head/><body><p>The name of the annotation which defines the exons in the mRNA sequence.</p></body></html></string> 3079 </property> 3080 <property name="text"> 3081 <string>exon</string> 3082 </property> 3083 </widget> 3084 </item> 3085 <item> 3086 <spacer name="horizontalSpacer_9"> 3087 <property name="orientation"> 3088 <enum>Qt::Horizontal</enum> 3089 </property> 3090 <property name="sizeHint" stdset="0"> 3091 <size> 3092 <width>40</width> 3093 <height>20</height> 3094 </size> 3095 </property> 3096 </spacer> 3097 </item> 3098 </layout> 3099 </item> 3100 </layout> 3101 </widget> 3102 </item> 3103 <item> 3104 <widget class="QGroupBox" name="spanJunctionBox"> 3105 <property name="title"> 3106 <string>Minimum exon junction overlap size</string> 3107 </property> 3108 <property name="checkable"> 3109 <bool>true</bool> 3110 </property> 3111 <property name="checked"> 3112 <bool>false</bool> 3113 </property> 3114 <layout class="QGridLayout" name="gridLayout_16"> 3115 <item row="0" column="0"> 3116 <widget class="QLabel" name="label_83"> 3117 <property name="text"> 3118 <string>At 5' side (bp):</string> 3119 </property> 3120 </widget> 3121 </item> 3122 <item row="0" column="1"> 3123 <widget class="QSpinBox" name="leftOverlapSizeSpinBox"> 3124 <property name="minimum"> 3125 <number>1</number> 3126 </property> 3127 <property name="value"> 3128 <number>5</number> 3129 </property> 3130 </widget> 3131 </item> 3132 <item row="0" column="2" rowspan="2"> 3133 <spacer name="horizontalSpacer_36"> 3134 <property name="orientation"> 3135 <enum>Qt::Horizontal</enum> 3136 </property> 3137 <property name="sizeHint" stdset="0"> 3138 <size> 3139 <width>760</width> 3140 <height>20</height> 3141 </size> 3142 </property> 3143 </spacer> 3144 </item> 3145 <item row="1" column="0"> 3146 <widget class="QLabel" name="label_84"> 3147 <property name="text"> 3148 <string>At 3'side (bp)</string> 3149 </property> 3150 </widget> 3151 </item> 3152 <item row="1" column="1"> 3153 <widget class="QSpinBox" name="rightOverlapSizeSpinBox"> 3154 <property name="minimum"> 3155 <number>1</number> 3156 </property> 3157 <property name="value"> 3158 <number>5</number> 3159 </property> 3160 </widget> 3161 </item> 3162 </layout> 3163 </widget> 3164 </item> 3165 <item> 3166 <layout class="QHBoxLayout" name="horizontalLayout_8"> 3167 <item> 3168 <widget class="QLabel" name="label_82"> 3169 <property name="text"> 3170 <string>Exon range:</string> 3171 </property> 3172 </widget> 3173 </item> 3174 <item> 3175 <widget class="QLineEdit" name="exonRangeEdit"> 3176 <property name="sizePolicy"> 3177 <sizepolicy hsizetype="Fixed" vsizetype="Fixed"> 3178 <horstretch>0</horstretch> 3179 <verstretch>0</verstretch> 3180 </sizepolicy> 3181 </property> 3182 <property name="toolTip"> 3183 <string><html><head/><body><p>If the range is set, primer search will be restricted to selected exons. For example:</p><p><span style=" font-weight:600;">1-5</span></p><p>If the range is larger than actual exon range or the starting exon number exceeds number of exons, error message is shown. </p></body></html></string> 3184 </property> 3185 </widget> 3186 </item> 3187 <item> 3188 <spacer name="horizontalSpacer_37"> 3189 <property name="orientation"> 3190 <enum>Qt::Horizontal</enum> 3191 </property> 3192 <property name="sizeHint" stdset="0"> 3193 <size> 3194 <width>40</width> 3195 <height>20</height> 3196 </size> 3197 </property> 3198 </spacer> 3199 </item> 3200 </layout> 3201 </item> 3202 <item> 3203 <widget class="QCheckBox" name="spanIntronCheckBox"> 3204 <property name="text"> 3205 <string>Primer product must span at least one intron on the corresponding genomic DNA</string> 3206 </property> 3207 <property name="checked"> 3208 <bool>true</bool> 3209 </property> 3210 </widget> 3211 </item> 3212 <item> 3213 <layout class="QHBoxLayout" name="horizontalLayout_7"> 3214 <item> 3215 <widget class="QLabel" name="label_10"> 3216 <property name="text"> 3217 <string>Max number of pairs to query:</string> 3218 </property> 3219 </widget> 3220 </item> 3221 <item> 3222 <widget class="QSpinBox" name="maxPairsBox"> 3223 <property name="toolTip"> 3224 <string><html><head/><body><p>This number of found primer pairs wil bel queried to check if they fullfill the requirements for RTPCR.</p></body></html></string> 3225 </property> 3226 <property name="minimum"> 3227 <number>100</number> 3228 </property> 3229 <property name="maximum"> 3230 <number>10000</number> 3231 </property> 3232 <property name="value"> 3233 <number>1000</number> 3234 </property> 3235 </widget> 3236 </item> 3237 <item> 3238 <spacer name="horizontalSpacer_17"> 3239 <property name="orientation"> 3240 <enum>Qt::Horizontal</enum> 3241 </property> 3242 <property name="sizeHint" stdset="0"> 3243 <size> 3244 <width>40</width> 3245 <height>20</height> 3246 </size> 3247 </property> 3248 </spacer> 3249 </item> 3250 </layout> 3251 </item> 3252 <item> 3253 <widget class="QLabel" name="warningLabel"> 3254 <property name="text"> 3255 <string/> 3256 </property> 3257 </widget> 3258 </item> 3259 </layout> 3260 </widget> 3261 </item> 3262 <item> 3263 <spacer name="verticalSpacer_7"> 3264 <property name="orientation"> 3265 <enum>Qt::Vertical</enum> 3266 </property> 3267 <property name="sizeHint" stdset="0"> 3268 <size> 3269 <width>20</width> 3270 <height>40</height> 3271 </size> 3272 </property> 3273 </spacer> 3274 </item> 3275 </layout> 3276 </widget> 3277 <widget class="QWidget" name="tab_SequenceQuality"> 3278 <attribute name="title"> 3279 <string>Sequence Quality</string> 3280 </attribute> 3281 <attribute name="toolTip"> 3282 <string><html><head/><body><p>In this section user can specify sequence quality of target sequence and related parameters.</p></body></html></string> 3283 </attribute> 3284 <layout class="QVBoxLayout" name="verticalLayout_2"> 3285 <item> 3286 <widget class="QLabel" name="label"> 3287 <property name="text"> 3288 <string>Sequence quality</string> 3289 </property> 3290 </widget> 3291 </item> 3292 <item> 3293 <widget class="QPlainTextEdit" name="edit_PRIMER_SEQUENCE_QUALITY"> 3294 <property name="toolTip"> 3295 <string><html><head/><body><p>A list of space separated integers. There must be exactly one integer for each base in the Source Sequence if this argument is non-empty. High numbers indicate high confidence in the base call at that position and low numbers indicate low confidence in the base call at that position.</p></body></html></string> 3296 </property> 3297 </widget> 3298 </item> 3299 <item> 3300 <layout class="QHBoxLayout" name="horizontalLayout_2"> 3301 <item> 3302 <widget class="QLabel" name="label_2"> 3303 <property name="text"> 3304 <string>Min sequence quality:</string> 3305 </property> 3306 </widget> 3307 </item> 3308 <item> 3309 <widget class="QSpinBox" name="edit_PRIMER_MIN_QUALITY"> 3310 <property name="sizePolicy"> 3311 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 3312 <horstretch>0</horstretch> 3313 <verstretch>0</verstretch> 3314 </sizepolicy> 3315 </property> 3316 <property name="toolTip"> 3317 <string><html><head/><body><p>The minimum sequence quality allowed within a primer.</p></body></html></string> 3318 </property> 3319 <property name="maximum"> 3320 <number>9999</number> 3321 </property> 3322 </widget> 3323 </item> 3324 <item> 3325 <widget class="QLabel" name="label_3"> 3326 <property name="text"> 3327 <string>Min 3' sequence quality:</string> 3328 </property> 3329 </widget> 3330 </item> 3331 <item> 3332 <widget class="QSpinBox" name="edit_PRIMER_MIN_END_QUALITY"> 3333 <property name="sizePolicy"> 3334 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 3335 <horstretch>0</horstretch> 3336 <verstretch>0</verstretch> 3337 </sizepolicy> 3338 </property> 3339 <property name="toolTip"> 3340 <string><html><head/><body><p>The minimum sequence quality allowed within the 3' pentamer of a primer.</p></body></html></string> 3341 </property> 3342 <property name="maximum"> 3343 <number>9999</number> 3344 </property> 3345 </widget> 3346 </item> 3347 <item> 3348 <widget class="QLabel" name="label_4"> 3349 <property name="text"> 3350 <string>Sequence quality range min:</string> 3351 </property> 3352 </widget> 3353 </item> 3354 <item> 3355 <widget class="QSpinBox" name="edit_PRIMER_QUALITY_RANGE_MIN"> 3356 <property name="sizePolicy"> 3357 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 3358 <horstretch>0</horstretch> 3359 <verstretch>0</verstretch> 3360 </sizepolicy> 3361 </property> 3362 <property name="toolTip"> 3363 <string><html><head/><body><p>The minimum legal sequence quality.</p></body></html></string> 3364 </property> 3365 <property name="maximum"> 3366 <number>9999</number> 3367 </property> 3368 </widget> 3369 </item> 3370 <item> 3371 <widget class="QLabel" name="label_5"> 3372 <property name="text"> 3373 <string>Sequence quality range max:</string> 3374 </property> 3375 </widget> 3376 </item> 3377 <item> 3378 <widget class="QSpinBox" name="edit_PRIMER_QUALITY_RANGE_MAX"> 3379 <property name="sizePolicy"> 3380 <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> 3381 <horstretch>0</horstretch> 3382 <verstretch>0</verstretch> 3383 </sizepolicy> 3384 </property> 3385 <property name="toolTip"> 3386 <string><html><head/><body><p>The maximum legal sequence quality.</p></body></html></string> 3387 </property> 3388 <property name="maximum"> 3389 <number>9999</number> 3390 </property> 3391 </widget> 3392 </item> 3393 </layout> 3394 </item> 3395 </layout> 3396 </widget> 3397 <widget class="QWidget" name="tab_Result"> 3398 <attribute name="title"> 3399 <string>Result Settings</string> 3400 </attribute> 3401 <attribute name="toolTip"> 3402 <string><html><head/><body><p>This section allows to set output annotations' settings.</p></body></html></string> 3403 </attribute> 3404 <layout class="QVBoxLayout" name="verticalLayout_46"> 3405 <item> 3406 <layout class="QVBoxLayout" name="annotationWidgetLayout"/> 3407 </item> 3408 <item> 3409 <spacer name="verticalSpacer_2"> 3410 <property name="orientation"> 3411 <enum>Qt::Vertical</enum> 3412 </property> 3413 <property name="sizeHint" stdset="0"> 3414 <size> 3415 <width>20</width> 3416 <height>40</height> 3417 </size> 3418 </property> 3419 </spacer> 3420 </item> 3421 </layout> 3422 </widget> 3423 </widget> 3424 </item> 3425 <item> 3426 <widget class="Line" name="line_6"> 3427 <property name="orientation"> 3428 <enum>Qt::Horizontal</enum> 3429 </property> 3430 </widget> 3431 </item> 3432 <item> 3433 <layout class="QHBoxLayout" name="horizontalLayout"> 3434 <item> 3435 <layout class="QHBoxLayout" name="rangeSelectorLayout"/> 3436 </item> 3437 <item> 3438 <spacer name="horizontalSpacer"> 3439 <property name="orientation"> 3440 <enum>Qt::Horizontal</enum> 3441 </property> 3442 <property name="sizeHint" stdset="0"> 3443 <size> 3444 <width>40</width> 3445 <height>20</height> 3446 </size> 3447 </property> 3448 </spacer> 3449 </item> 3450 </layout> 3451 </item> 3452 <item> 3453 <layout class="QHBoxLayout" name="horizontalLayout_6"> 3454 <item> 3455 <widget class="QPushButton" name="helpButton"> 3456 <property name="text"> 3457 <string>Help</string> 3458 </property> 3459 </widget> 3460 </item> 3461 <item> 3462 <spacer name="horizontalSpacer_14"> 3463 <property name="orientation"> 3464 <enum>Qt::Horizontal</enum> 3465 </property> 3466 <property name="sizeHint" stdset="0"> 3467 <size> 3468 <width>40</width> 3469 <height>20</height> 3470 </size> 3471 </property> 3472 </spacer> 3473 </item> 3474 <item> 3475 <widget class="QPushButton" name="saveSettingsButton"> 3476 <property name="text"> 3477 <string>Save settings</string> 3478 </property> 3479 </widget> 3480 </item> 3481 <item> 3482 <widget class="QPushButton" name="loadSettingsButton"> 3483 <property name="text"> 3484 <string>Load settings</string> 3485 </property> 3486 </widget> 3487 </item> 3488 <item> 3489 <widget class="QPushButton" name="resetButton"> 3490 <property name="text"> 3491 <string>Reset form</string> 3492 </property> 3493 </widget> 3494 </item> 3495 <item> 3496 <widget class="QPushButton" name="pickPrimersButton"> 3497 <property name="text"> 3498 <string>Pick primers</string> 3499 </property> 3500 </widget> 3501 </item> 3502 </layout> 3503 </item> 3504 </layout> 3505 </widget> 3506 <tabstops> 3507 <tabstop>edit_EXCLUDED_REGION</tabstop> 3508 <tabstop>edit_TARGET</tabstop> 3509 <tabstop>edit_PRIMER_PRODUCT_SIZE_RANGE</tabstop> 3510 <tabstop>combobox_PRIMER_MISPRIMING_LIBRARY</tabstop> 3511 <tabstop>edit_PRIMER_NUM_RETURN</tabstop> 3512 <tabstop>edit_PRIMER_MAX_END_STABILITY</tabstop> 3513 <tabstop>edit_PRIMER_MAX_MISPRIMING</tabstop> 3514 <tabstop>edit_PRIMER_PAIR_MAX_MISPRIMING</tabstop> 3515 <tabstop>edit_PRIMER_MAX_TEMPLATE_MISPRIMING</tabstop> 3516 <tabstop>edit_PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING</tabstop> 3517 <tabstop>checkbox_PICK_LEFT</tabstop> 3518 <tabstop>edit_PRIMER_LEFT_INPUT</tabstop> 3519 <tabstop>checkbox_PICK_HYBRO</tabstop> 3520 <tabstop>edit_PRIMER_INTERNAL_OLIGO_INPUT</tabstop> 3521 <tabstop>checkbox_PICK_RIGHT</tabstop> 3522 <tabstop>edit_PRIMER_RIGHT_INPUT</tabstop> 3523 <tabstop>tabWidget</tabstop> 3524 <tabstop>edit_PRIMER_MIN_SIZE</tabstop> 3525 <tabstop>edit_PRIMER_OPT_SIZE</tabstop> 3526 <tabstop>edit_PRIMER_MAX_SIZE</tabstop> 3527 <tabstop>edit_PRIMER_MIN_TM</tabstop> 3528 <tabstop>edit_PRIMER_OPT_TM</tabstop> 3529 <tabstop>edit_PRIMER_MAX_TM</tabstop> 3530 <tabstop>edit_PRIMER_PRODUCT_MIN_TM</tabstop> 3531 <tabstop>edit_PRIMER_PRODUCT_OPT_TM</tabstop> 3532 <tabstop>edit_PRIMER_PRODUCT_MAX_TM</tabstop> 3533 <tabstop>edit_PRIMER_MIN_GC</tabstop> 3534 <tabstop>edit_PRIMER_OPT_GC_PERCENT</tabstop> 3535 <tabstop>edit_PRIMER_MAX_GC</tabstop> 3536 <tabstop>edit_PRIMER_SELF_ANY</tabstop> 3537 <tabstop>edit_PRIMER_SELF_END</tabstop> 3538 <tabstop>edit_PRIMER_NUM_NS_ACCEPTED</tabstop> 3539 <tabstop>edit_PRIMER_MAX_POLY_X</tabstop> 3540 <tabstop>edit_PRIMER_INSIDE_PENALTY</tabstop> 3541 <tabstop>edit_PRIMER_OUTSIDE_PENALTY</tabstop> 3542 <tabstop>edit_PRIMER_FIRST_BASE_INDEX</tabstop> 3543 <tabstop>edit_PRIMER_GC_CLAMP</tabstop> 3544 <tabstop>edit_PRIMER_SALT_CONC</tabstop> 3545 <tabstop>combobox_PRIMER_SALT_CORRECTIONS</tabstop> 3546 <tabstop>edit_PRIMER_DIVALENT_CONC</tabstop> 3547 <tabstop>edit_PRIMER_DNTP_CONC</tabstop> 3548 <tabstop>edit_PRIMER_DNA_CONC</tabstop> 3549 <tabstop>checkbox_PRIMER_LIBERAL_BASE</tabstop> 3550 <tabstop>checkbox_SHOW_DEBUGGING</tabstop> 3551 <tabstop>checkbox_PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS</tabstop> 3552 <tabstop>checkbox_PRIMER_LOWERCASE_MASKING</tabstop> 3553 <tabstop>edit_PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION</tabstop> 3554 <tabstop>edit_PRIMER_INTERNAL_OLIGO_MIN_SIZE</tabstop> 3555 <tabstop>edit_PRIMER_INTERNAL_OLIGO_OPT_SIZE</tabstop> 3556 <tabstop>edit_PRIMER_INTERNAL_OLIGO_MAX_SIZE</tabstop> 3557 <tabstop>edit_PRIMER_INTERNAL_OLIGO_MIN_TM</tabstop> 3558 <tabstop>edit_PRIMER_INTERNAL_OLIGO_OPT_TM</tabstop> 3559 <tabstop>edit_PRIMER_INTERNAL_OLIGO_MAX_TM</tabstop> 3560 <tabstop>edit_PRIMER_INTERNAL_OLIGO_MIN_GC</tabstop> 3561 <tabstop>edit_PRIMER_INTERNAL_OLIGO_OPT_GC_PERCENT</tabstop> 3562 <tabstop>edit_PRIMER_INTERNAL_OLIGO_MAX_GC</tabstop> 3563 <tabstop>edit_PRIMER_INTERNAL_OLIGO_SELF_ANY</tabstop> 3564 <tabstop>edit_PRIMER_INTERNAL_OLIGO_SELF_END</tabstop> 3565 <tabstop>edit_PRIMER_INTERNAL_OLIGO_NUM_NS</tabstop> 3566 <tabstop>edit_PRIMER_INTERNAL_OLIGO_MAX_POLY_X</tabstop> 3567 <tabstop>combobox_PRIMER_INTERNAL_OLIGO_MISHYB_LIBRARY</tabstop> 3568 <tabstop>edit_PRIMER_INTERNAL_OLIGO_MAX_MISHYB</tabstop> 3569 <tabstop>edit_PRIMER_INTERNAL_OLIGO_MIN_QUALITY</tabstop> 3570 <tabstop>edit_PRIMER_INTERNAL_OLIGO_SALT_CONC</tabstop> 3571 <tabstop>edit_PRIMER_INTERNAL_OLIGO_DNA_CONC</tabstop> 3572 <tabstop>edit_PRIMER_INTERNAL_OLIGO_DIVALENT_CONC</tabstop> 3573 <tabstop>edit_PRIMER_INTERNAL_OLIGO_DNTP_CONC</tabstop> 3574 <tabstop>edit_PRIMER_WT_TM_LT</tabstop> 3575 <tabstop>edit_PRIMER_WT_TM_GT</tabstop> 3576 <tabstop>edit_PRIMER_WT_SIZE_LT</tabstop> 3577 <tabstop>edit_PRIMER_WT_SIZE_GT</tabstop> 3578 <tabstop>edit_PRIMER_WT_GC_PERCENT_LT</tabstop> 3579 <tabstop>edit_PRIMER_WT_GC_PERCENT_GT</tabstop> 3580 <tabstop>edit_PRIMER_WT_COMPL_ANY</tabstop> 3581 <tabstop>edit_PRIMER_WT_COMPL_END</tabstop> 3582 <tabstop>edit_PRIMER_WT_NUM_NS</tabstop> 3583 <tabstop>edit_PRIMER_WT_REP_SIM</tabstop> 3584 <tabstop>edit_PRIMER_WT_SEQ_QUAL</tabstop> 3585 <tabstop>edit_PRIMER_WT_END_QUAL</tabstop> 3586 <tabstop>edit_PRIMER_WT_POS_PENALTY</tabstop> 3587 <tabstop>edit_PRIMER_WT_END_STABILITY</tabstop> 3588 <tabstop>edit_PRIMER_WT_TEMPLATE_MISPRIMING</tabstop> 3589 <tabstop>edit_PRIMER_PAIR_WT_PRODUCT_SIZE_LT</tabstop> 3590 <tabstop>edit_PRIMER_PAIR_WT_PRODUCT_SIZE_GT</tabstop> 3591 <tabstop>edit_PRIMER_PAIR_WT_PRODUCT_TM_LT</tabstop> 3592 <tabstop>edit_PRIMER_PAIR_WT_PRODUCT_TM_GT</tabstop> 3593 <tabstop>edit_PRIMER_PAIR_WT_DIFF_TM</tabstop> 3594 <tabstop>edit_PRIMER_PAIR_WT_COMPL_ANY</tabstop> 3595 <tabstop>edit_PRIMER_PAIR_WT_COMPL_END</tabstop> 3596 <tabstop>edit_PRIMER_PAIR_WT_REP_SIM</tabstop> 3597 <tabstop>edit_PRIMER_PAIR_WT_PR_PENALTY</tabstop> 3598 <tabstop>edit_PRIMER_PAIR_WT_IO_PENALTY</tabstop> 3599 <tabstop>edit_PRIMER_PAIR_WT_TEMPLATE_MISPRIMING</tabstop> 3600 <tabstop>edit_PRIMER_IO_WT_TM_LT</tabstop> 3601 <tabstop>edit_PRIMER_IO_WT_TM_GT</tabstop> 3602 <tabstop>edit_PRIMER_IO_WT_SIZE_LT</tabstop> 3603 <tabstop>edit_PRIMER_IO_WT_SIZE_GT</tabstop> 3604 <tabstop>edit_PRIMER_IO_WT_GC_PERCENT_LT</tabstop> 3605 <tabstop>edit_PRIMER_IO_WT_GC_PERCENT_GT</tabstop> 3606 <tabstop>edit_PRIMER_IO_WT_COMPL_ANY</tabstop> 3607 <tabstop>edit_PRIMER_IO_WT_NUM_NS</tabstop> 3608 <tabstop>edit_PRIMER_IO_WT_REP_SIM</tabstop> 3609 <tabstop>edit_PRIMER_IO_WT_SEQ_QUAL</tabstop> 3610 <tabstop>edit_PRIMER_SEQUENCE_QUALITY</tabstop> 3611 <tabstop>edit_PRIMER_MIN_QUALITY</tabstop> 3612 <tabstop>edit_PRIMER_MIN_END_QUALITY</tabstop> 3613 <tabstop>edit_PRIMER_QUALITY_RANGE_MIN</tabstop> 3614 <tabstop>edit_PRIMER_QUALITY_RANGE_MAX</tabstop> 3615 </tabstops> 3616 <resources/> 3617 <connections> 3618 <connection> 3619 <sender>checkbox_PICK_HYBRO</sender> 3620 <signal>clicked(bool)</signal> 3621 <receiver>edit_PRIMER_INTERNAL_OLIGO_INPUT</receiver> 3622 <slot>setEnabled(bool)</slot> 3623 <hints> 3624 <hint type="sourcelabel"> 3625 <x>404</x> 3626 <y>558</y> 3627 </hint> 3628 <hint type="destinationlabel"> 3629 <x>404</x> 3630 <y>583</y> 3631 </hint> 3632 </hints> 3633 </connection> 3634 <connection> 3635 <sender>checkbox_PICK_LEFT</sender> 3636 <signal>clicked(bool)</signal> 3637 <receiver>edit_PRIMER_LEFT_INPUT</receiver> 3638 <slot>setEnabled(bool)</slot> 3639 <hints> 3640 <hint type="sourcelabel"> 3641 <x>133</x> 3642 <y>558</y> 3643 </hint> 3644 <hint type="destinationlabel"> 3645 <x>133</x> 3646 <y>583</y> 3647 </hint> 3648 </hints> 3649 </connection> 3650 <connection> 3651 <sender>checkbox_PICK_RIGHT</sender> 3652 <signal>clicked(bool)</signal> 3653 <receiver>edit_PRIMER_RIGHT_INPUT</receiver> 3654 <slot>setEnabled(bool)</slot> 3655 <hints> 3656 <hint type="sourcelabel"> 3657 <x>743</x> 3658 <y>558</y> 3659 </hint> 3660 <hint type="destinationlabel"> 3661 <x>743</x> 3662 <y>583</y> 3663 </hint> 3664 </hints> 3665 </connection> 3666 </connections> 3667</ui> 3668