1 2<a name="output.1"></a> 3<h3>Output files for usage example </h3> 4<p><h3>File: needleall.error</h3> 5<table width="90%"><tr><td bgcolor="#CCFFCC"> 6<pre> 7Alignment score (21.5) is less than minimum score(40.0) for sequences Illumina_Genomici_DNA_Adapters1_1 vs FC12044_91407_8_200_406_24 8Alignment score (24.5) is less than minimum score(40.0) for sequences Illumina_Genomic_DNA_Adapters1_2 vs FC12044_91407_8_200_406_24 9Alignment score (31.0) is less than minimum score(40.0) for sequences Illumina_Genomic_DNA_PCR_Primers1_1 vs FC12044_91407_8_200_406_24 10Alignment score (25.5) is less than minimum score(40.0) for sequences Illumina_Genomic_DNA_PCR_Primers1_2 vs FC12044_91407_8_200_406_24 11Alignment score (24.5) is less than minimum score(40.0) for sequences Illumina_Genomic_DNA_sequencing_primer vs FC12044_91407_8_200_406_24 12Alignment score (16.5) is less than minimum score(40.0) for sequences Illumina_Paired_End_DNA_Adapters1_1 vs FC12044_91407_8_200_406_24 13Alignment score (24.5) is less than minimum score(40.0) for sequences Illumina_Paired_End_DNA_Adapters1_2 vs FC12044_91407_8_200_406_24 14Alignment score (31.0) is less than minimum score(40.0) for sequences Illumina_Paired_End_DNA_PCR_Primers1_1 vs FC12044_91407_8_200_406_24 15Alignment score (21.0) is less than minimum score(40.0) for sequences Illumina_Paired_End_DNA_PCR_Primers1_2 vs FC12044_91407_8_200_406_24 16Alignment score (24.5) is less than minimum score(40.0) for sequences Illumina_Paired_End_DNA_sequencing_primer_1 vs FC12044_91407_8_200_406_24 17Alignment score (21.0) is less than minimum score(40.0) for sequences Illumina_Paired_End_DNA_sequencing_primer_2 vs FC12044_91407_8_200_406_24 18Alignment score (14.5) is less than minimum score(40.0) for sequences Illumina_DpnII_Gex_Adapters1_1 vs FC12044_91407_8_200_406_24 19Alignment score (24.5) is less than minimum score(40.0) for sequences Illumina_DpnII_Gex_Adapters1_2 vs FC12044_91407_8_200_406_24 20Alignment score (12.0) is less than minimum score(40.0) for sequences Illumina_DpnII_Gex_Adapters2_1 vs FC12044_91407_8_200_406_24 21Alignment score (12.0) is less than minimum score(40.0) for sequences Illumina_DpnII_Gex_Adapters2_2 vs FC12044_91407_8_200_406_24 22Alignment score (12.0) is less than minimum score(40.0) for sequences Illumina_DpnII_Gex_PCR_Primer_1 vs FC12044_91407_8_200_406_24 23Alignment score (23.5) is less than minimum score(40.0) for sequences Illumina_DpnII_Gex_sequencing_primer vs FC12044_91407_8_200_406_24 24Alignment score (12.5) is less than minimum score(40.0) for sequences Illumina_NlaIII_Gex_Adapters1_1 vs FC12044_91407_8_200_406_24 25Alignment score (27.0) is less than minimum score(40.0) for sequences Illumina_NlaIII_Gex_Adapters1_2 vs FC12044_91407_8_200_406_24 26Alignment score (12.0) is less than minimum score(40.0) for sequences Illumina_NlaIII_Gex_Adapters2_1 vs FC12044_91407_8_200_406_24 27Alignment score (12.0) is less than minimum score(40.0) for sequences Illumina_NlaIII_Gex_Adapters2_2 vs FC12044_91407_8_200_406_24 28Alignment score (12.0) is less than minimum score(40.0) for sequences Illumina_NlaIII_Gex_PCR_Primer_1 vs FC12044_91407_8_200_406_24 29Alignment score (27.5) is less than minimum score(40.0) for sequences Illumina_NlaIII_Gex_sequencing_primer vs FC12044_91407_8_200_406_24 30Alignment score (12.0) is less than minimum score(40.0) for sequences Illumina_Small_RNA_RT_Primer vs FC12044_91407_8_200_406_24 31Alignment score (23.5) is less than minimum score(40.0) for sequences Illumina_Small_RNA_5p_Adapter vs FC12044_91407_8_200_406_24 32Alignment score (13.0) is less than minimum score(40.0) for sequences Illumina_Small_RNA_3p_Adapter vs FC12044_91407_8_200_406_24 33Alignment score (12.0) is less than minimum score(40.0) for sequences Illumina_Small_RNA_PCR_Primer_1 vs FC12044_91407_8_200_406_24 34Alignment score (23.5) is less than minimum score(40.0) for sequences Illumina_Small_RNA_sequencing_primer vs FC12044_91407_8_200_406_24 35Alignment score (17.5) is less than minimum score(40.0) for sequences Illumina_Genomici_DNA_Adapters1_1 vs FC12044_91407_8_200_720_610 36Alignment score (31.5) is less than minimum score(40.0) for sequences Illumina_Genomic_DNA_Adapters1_2 vs FC12044_91407_8_200_720_610 37Alignment score (31.5) is less than minimum score(40.0) for sequences Illumina_Genomic_DNA_PCR_Primers1_1 vs FC12044_91407_8_200_720_610 38Alignment score (20.5) is less than minimum score(40.0) for sequences Illumina_Genomic_DNA_PCR_Primers1_2 vs FC12044_91407_8_200_720_610 39Alignment score (31.5) is less than minimum score(40.0) for sequences Illumina_Genomic_DNA_sequencing_primer vs FC12044_91407_8_200_720_610 40Alignment score (0.0) is less than minimum score(40.0) for sequences Illumina_Paired_End_DNA_Adapters1_1 vs FC12044_91407_8_200_720_610 41Alignment score (31.5) is less than minimum score(40.0) for sequences Illumina_Paired_End_DNA_Adapters1_2 vs FC12044_91407_8_200_720_610 42Alignment score (31.5) is less than minimum score(40.0) for sequences Illumina_Paired_End_DNA_PCR_Primers1_1 vs FC12044_91407_8_200_720_610 43Alignment score (33.5) is less than minimum score(40.0) for sequences Illumina_Paired_End_DNA_PCR_Primers1_2 vs FC12044_91407_8_200_720_610 44Alignment score (31.5) is less than minimum score(40.0) for sequences Illumina_Paired_End_DNA_sequencing_primer_1 vs FC12044_91407_8_200_720_610 45Alignment score (33.5) is less than minimum score(40.0) for sequences Illumina_Paired_End_DNA_sequencing_primer_2 vs FC12044_91407_8_200_720_610 46Alignment score (20.0) is less than minimum score(40.0) for sequences Illumina_DpnII_Gex_Adapters1_1 vs FC12044_91407_8_200_720_610 47Alignment score (9.0) is less than minimum score(40.0) for sequences Illumina_DpnII_Gex_Adapters1_2 vs FC12044_91407_8_200_720_610 48Alignment score (11.0) is less than minimum score(40.0) for sequences Illumina_DpnII_Gex_Adapters2_1 vs FC12044_91407_8_200_720_610 49Alignment score (15.5) is less than minimum score(40.0) for sequences Illumina_DpnII_Gex_Adapters2_2 vs FC12044_91407_8_200_720_610 50Alignment score (11.0) is less than minimum score(40.0) for sequences Illumina_DpnII_Gex_PCR_Primer_1 vs FC12044_91407_8_200_720_610 51Alignment score (10.0) is less than minimum score(40.0) for sequences Illumina_DpnII_Gex_PCR_Primer_2 vs FC12044_91407_8_200_720_610 52Alignment score (15.0) is less than minimum score(40.0) for sequences Illumina_DpnII_Gex_sequencing_primer vs FC12044_91407_8_200_720_610 53Alignment score (20.0) is less than minimum score(40.0) for sequences Illumina_NlaIII_Gex_Adapters1_1 vs FC12044_91407_8_200_720_610 54Alignment score (9.5) is less than minimum score(40.0) for sequences Illumina_NlaIII_Gex_Adapters1_2 vs FC12044_91407_8_200_720_610 55Alignment score (7.0) is less than minimum score(40.0) for sequences Illumina_NlaIII_Gex_Adapters2_1 vs FC12044_91407_8_200_720_610 56Alignment score (15.5) is less than minimum score(40.0) for sequences Illumina_NlaIII_Gex_Adapters2_2 vs FC12044_91407_8_200_720_610 57 58 59<font color=red> [Part of this file has been deleted for brevity]</font> 60 61Alignment score (13.0) is less than minimum score(40.0) for sequences Illumina_DpnII_Gex_Adapters1_1 vs FC12044_91407_8_200_675_16 62Alignment score (17.0) is less than minimum score(40.0) for sequences Illumina_DpnII_Gex_Adapters1_2 vs FC12044_91407_8_200_675_16 63Alignment score (13.5) is less than minimum score(40.0) for sequences Illumina_DpnII_Gex_Adapters2_1 vs FC12044_91407_8_200_675_16 64Alignment score (11.0) is less than minimum score(40.0) for sequences Illumina_DpnII_Gex_Adapters2_2 vs FC12044_91407_8_200_675_16 65Alignment score (13.5) is less than minimum score(40.0) for sequences Illumina_DpnII_Gex_PCR_Primer_1 vs FC12044_91407_8_200_675_16 66Alignment score (17.5) is less than minimum score(40.0) for sequences Illumina_DpnII_Gex_PCR_Primer_2 vs FC12044_91407_8_200_675_16 67Alignment score (22.0) is less than minimum score(40.0) for sequences Illumina_DpnII_Gex_sequencing_primer vs FC12044_91407_8_200_675_16 68Alignment score (13.0) is less than minimum score(40.0) for sequences Illumina_NlaIII_Gex_Adapters1_1 vs FC12044_91407_8_200_675_16 69Alignment score (17.0) is less than minimum score(40.0) for sequences Illumina_NlaIII_Gex_Adapters1_2 vs FC12044_91407_8_200_675_16 70Alignment score (13.5) is less than minimum score(40.0) for sequences Illumina_NlaIII_Gex_Adapters2_1 vs FC12044_91407_8_200_675_16 71Alignment score (11.0) is less than minimum score(40.0) for sequences Illumina_NlaIII_Gex_Adapters2_2 vs FC12044_91407_8_200_675_16 72Alignment score (13.5) is less than minimum score(40.0) for sequences Illumina_NlaIII_Gex_PCR_Primer_1 vs FC12044_91407_8_200_675_16 73Alignment score (17.5) is less than minimum score(40.0) for sequences Illumina_NlaIII_Gex_PCR_Primer_2 vs FC12044_91407_8_200_675_16 74Alignment score (21.5) is less than minimum score(40.0) for sequences Illumina_NlaIII_Gex_sequencing_primer vs FC12044_91407_8_200_675_16 75Alignment score (13.5) is less than minimum score(40.0) for sequences Illumina_Small_RNA_RT_Primer vs FC12044_91407_8_200_675_16 76Alignment score (15.0) is less than minimum score(40.0) for sequences Illumina_Small_RNA_5p_Adapter vs FC12044_91407_8_200_675_16 77Alignment score (7.0) is less than minimum score(40.0) for sequences Illumina_Small_RNA_3p_Adapter vs FC12044_91407_8_200_675_16 78Alignment score (13.5) is less than minimum score(40.0) for sequences Illumina_Small_RNA_PCR_Primer_1 vs FC12044_91407_8_200_675_16 79Alignment score (17.5) is less than minimum score(40.0) for sequences Illumina_Small_RNA_PCR_Primer_2 vs FC12044_91407_8_200_675_16 80Alignment score (22.0) is less than minimum score(40.0) for sequences Illumina_Small_RNA_sequencing_primer vs FC12044_91407_8_200_675_16 81Alignment score (21.0) is less than minimum score(40.0) for sequences Illumina_Genomici_DNA_Adapters1_1 vs FC12044_91407_8_200_285_136 82Alignment score (17.5) is less than minimum score(40.0) for sequences Illumina_Genomic_DNA_Adapters1_2 vs FC12044_91407_8_200_285_136 83Alignment score (30.0) is less than minimum score(40.0) for sequences Illumina_Genomic_DNA_PCR_Primers1_1 vs FC12044_91407_8_200_285_136 84Alignment score (16.5) is less than minimum score(40.0) for sequences Illumina_Genomic_DNA_PCR_Primers1_2 vs FC12044_91407_8_200_285_136 85Alignment score (17.5) is less than minimum score(40.0) for sequences Illumina_Genomic_DNA_sequencing_primer vs FC12044_91407_8_200_285_136 86Alignment score (7.0) is less than minimum score(40.0) for sequences Illumina_Paired_End_DNA_Adapters1_1 vs FC12044_91407_8_200_285_136 87Alignment score (17.5) is less than minimum score(40.0) for sequences Illumina_Paired_End_DNA_Adapters1_2 vs FC12044_91407_8_200_285_136 88Alignment score (30.0) is less than minimum score(40.0) for sequences Illumina_Paired_End_DNA_PCR_Primers1_1 vs FC12044_91407_8_200_285_136 89Alignment score (21.0) is less than minimum score(40.0) for sequences Illumina_Paired_End_DNA_PCR_Primers1_2 vs FC12044_91407_8_200_285_136 90Alignment score (17.5) is less than minimum score(40.0) for sequences Illumina_Paired_End_DNA_sequencing_primer_1 vs FC12044_91407_8_200_285_136 91Alignment score (18.5) is less than minimum score(40.0) for sequences Illumina_Paired_End_DNA_sequencing_primer_2 vs FC12044_91407_8_200_285_136 92Alignment score (27.5) is less than minimum score(40.0) for sequences Illumina_DpnII_Gex_Adapters1_1 vs FC12044_91407_8_200_285_136 93Alignment score (13.5) is less than minimum score(40.0) for sequences Illumina_DpnII_Gex_Adapters1_2 vs FC12044_91407_8_200_285_136 94Alignment score (6.0) is less than minimum score(40.0) for sequences Illumina_DpnII_Gex_Adapters2_1 vs FC12044_91407_8_200_285_136 95Alignment score (17.5) is less than minimum score(40.0) for sequences Illumina_DpnII_Gex_Adapters2_2 vs FC12044_91407_8_200_285_136 96Alignment score (6.0) is less than minimum score(40.0) for sequences Illumina_DpnII_Gex_PCR_Primer_1 vs FC12044_91407_8_200_285_136 97Alignment score (12.0) is less than minimum score(40.0) for sequences Illumina_DpnII_Gex_PCR_Primer_2 vs FC12044_91407_8_200_285_136 98Alignment score (17.5) is less than minimum score(40.0) for sequences Illumina_DpnII_Gex_sequencing_primer vs FC12044_91407_8_200_285_136 99Alignment score (26.5) is less than minimum score(40.0) for sequences Illumina_NlaIII_Gex_Adapters1_1 vs FC12044_91407_8_200_285_136 100Alignment score (14.5) is less than minimum score(40.0) for sequences Illumina_NlaIII_Gex_Adapters1_2 vs FC12044_91407_8_200_285_136 101Alignment score (2.0) is less than minimum score(40.0) for sequences Illumina_NlaIII_Gex_Adapters2_1 vs FC12044_91407_8_200_285_136 102Alignment score (17.5) is less than minimum score(40.0) for sequences Illumina_NlaIII_Gex_Adapters2_2 vs FC12044_91407_8_200_285_136 103Alignment score (6.0) is less than minimum score(40.0) for sequences Illumina_NlaIII_Gex_PCR_Primer_1 vs FC12044_91407_8_200_285_136 104Alignment score (12.0) is less than minimum score(40.0) for sequences Illumina_NlaIII_Gex_PCR_Primer_2 vs FC12044_91407_8_200_285_136 105Alignment score (15.5) is less than minimum score(40.0) for sequences Illumina_NlaIII_Gex_sequencing_primer vs FC12044_91407_8_200_285_136 106Alignment score (6.0) is less than minimum score(40.0) for sequences Illumina_Small_RNA_RT_Primer vs FC12044_91407_8_200_285_136 107Alignment score (15.5) is less than minimum score(40.0) for sequences Illumina_Small_RNA_5p_Adapter vs FC12044_91407_8_200_285_136 108Alignment score (17.5) is less than minimum score(40.0) for sequences Illumina_Small_RNA_3p_Adapter vs FC12044_91407_8_200_285_136 109Alignment score (6.0) is less than minimum score(40.0) for sequences Illumina_Small_RNA_PCR_Primer_1 vs FC12044_91407_8_200_285_136 110Alignment score (12.0) is less than minimum score(40.0) for sequences Illumina_Small_RNA_PCR_Primer_2 vs FC12044_91407_8_200_285_136 111Alignment score (17.5) is less than minimum score(40.0) for sequences Illumina_Small_RNA_sequencing_primer vs FC12044_91407_8_200_285_136 112</pre> 113</td></tr></table><p> 114