Target

Newly predicted signatures for a number of bacterial and viral pathogens. “Size of MSC soln” is the minimal (or near-minimal) number of signatures such each sequenced genome should be detected by one or more signatures, so that the set of signatures should in combination detect all the targets. Some additional signatures are provided which are not part of an MSC solution, as indicated by N, in cases where these signatures are predicted to detect a large fraction, but not all, of the target sequences. The predicted number of true positives is indicated. There were no false positives except for 2 of the Newcastle disease virus signatures, as indicated in the footnote. In some cases, more than one alternative signature is given that is predicted to detect the same set or subset of target sequences, as indicated by the same “group#” in the Signature ID for a given target organism (identical group#’s are followed by a unique signature # for a given organism). Different group#’s are predicted to detect different subsets of the target sequences. In some cases, alternative MSC solutions are provided. Amplicons in the predicted targets are provided as supplementary information on the web (Predicted_Amplicons_pathogen_sigs.xls). There was no single species-level signature for Dengue virus, so to detect the species requires a minimal set of 5 signatures, to detect any/all of the serotypes. # Genomes available Size of MSC soln If not part of MSC soln=N NCBI Taxonomy node Target organism Viruses Dengue 1 Dengue 2 True positives Signature ID Forward Primer Probe Reverse Pri 11053 11060 47 57 1 2 47 28 39 group469_64 group57_661 group287_278 group598_3392 group1215_3979 group544_1654 group544_2584 group30_2087 group1_11 group1_17 group1_25 group1_45 group1_7 group31_178 GCCATAGTACGGAAAGAGCTATGC CACGTGTGACATGCCACATC TAGGTCGCCTGATCACAGTCA CTTCCAGGCCCCTTCTGA ATGATTGGTGCATTGCTCTGA AGGCTGCAAACCGTGGAA GACCTTAATAGCCCCCGACTTCT GTGGACCGACGAGGACAGT TTCCGGAACCGCCTACAA TTTCTTACATGGGCATCTTGCAT CCGGACCCCACATGATTT CAGAGTATCCACACAGGATGCA GAGGCTGGTTTAATATACAACGCTTT GAAGAAGAACGATGGGAATCATAATC CTGTGAGCCCCGTCCAAGGACG TTTGCTTGATTCTGTAGGCTCCATCTTCCA AGCAGAACCTCCATTCGGAGACAGCTACAT CCACATGTGGAACGAGCGCCAC AGCTGCTTCACCCATCTCTACTCGAGTTGA TGGTTAGAGGAGACCCCTCCCATGACA CAATTTCATTGGTCCTTGGCCATTCAGC CAAATCGGAAGCTTGCTTAACACAGTTCTAACAGTT CACCAAAAGGCGCTCCTAATGCTTCA CGAGACTGCATTTACCTTTTCCTGTTACATACCTG CTGCTAGAACAAGCCGCTCTCACCG ACCAAGCCATGCTATGCAGGCAGC CGTGGCACGCTATAACAGTACCAATGTGC TCGCTCCGTGCGACTGCTGTTT CAGCTTCCATG CCCATGGGAAA TGTCCCGGGTC OR alternate MSC soln 2 Dengue 3 Dengue 4 Human adenoA 11069 11070 129875 70 11 1 1 1 1 55 56 70 70 11 1 1 1 1 1 Human adenoB 108098 20 2 18 CGTCCACATGG CCAGCAAGCAT AAGGAGGTACA GGCGAAGAGAT GGGTTGATACG GGCGCCTGAGC CAAACACCCAT GAGGGTTAAGT TGTATTCCTCC GAGCCAGCGCC TTAAGGGCTAT 18 18 12 Human adenoC Human adenoD 129951 130310 6 6 1 1 6 6 6 6 6 6 Human adenoE 130308 12 1 2 12 9 3 3 Human adenoF 130309 2 1 2 2 2 Canine distemper virus 11232 11 1 11 11 11 11 11 Coxsackie B4 12073 3 2 2 2 1 1 Cytomegalovirus HumanHerpes1 10358 10298 7 1 1 1 7 1 1 1 1 1 HumanHerpes2 10310 1 1 1 1 group31_181 group31_369 group38_266 group1_33 group1_40 group10_116 group10_160 group10_225 group10_31 group6_10 group7_1 group9_104 group9_58 group3_113 group3_34 group3_62 group1_1 group1_225 group1_141 group1_186 group1_211 group1_12 group1_7 group2_5 group2_1 group14_2521 group1_11 group1_12 group1_14 group1_1 group1_8 group1_12 group1_13 TCAAAAACACACTACCCACATACATG CAAGTGATTCATGGTCGAGAGAA CCCACTATGTACAGTTCTATGAATCGA AGTAGTATAGCCCCACCACCACAT CCCTGTAGCCGGAGGGTTA ACGCATGCAAGGTGTGGTT ACCAGCCCATTTCACAGTGTAA GCCCAGGTGTTGCCACTTA AGCTGCGGACTCATCTACTTTGA GGCACAGGGAACTCTTGCA CAAGCCCTGGCCTGAGTT TAGAGGCCCACCGAAGCA TTCAGAGCAGGACTCATGGAGAT TCCAACATGCAACAAACGTACAC GCTTTTCCCATTTAGACAATATCATGT CATTTATTACACCCCCGTTTGC TCCCTCATGATGCTATATCAACAGAT GGGCATGATCCGCTCATC TTTGTGTCAACAGAGGCCTACCT GGCGAACTGCAGGTGTCA CTACCCCATGTGCAACCAAA CTCTCTCCACGGACTCTTCTGTT GCACTACAGGTATGTTGTTGATGACA AATCTGTGGAGCGAGCAATG GGTATACGATCCACGTACAATGCA TGTTTACGGATATACCGGAACGA GGAGACCCCAAAACGACAGA TGTGTATGGCGTCCCATCTG CTCACCGGCGGCTAAGTC AACACATACACATGGCCCCTTT CGGGTAAGTAACAGAGTCTGACTAAGG AGCTGACGGCCAGTCACA CTCTCTTGCCGGGTTTTAGTCT TCTCTTTTGGCATGTGCATATTAACAATCTGTCTG TCTTCATTGTCATTGTAATCAGCAGGGTTCACT TGCCCTTGACATGAGGCAGCTTCTTAA CAAACTCACAGAACCCTAGTATTCAACCTGCCA TCATGCAAGACCCCGCTTGCA TCCTATATAAGTGGCAACACCTGGGCACTG CACAGTTTCCTGGCGAGCCAAACG AGGACTAAGCCCCGCCCATGAGTCAT CCCAACGGTCCTGCACACGGA CCTCGCACGGAACTTACATTGTGCATG CAATGTCATGACCAGGTGCAATATGCATC CAGGTAAGAGACCCCCTCCGATGAGTTCT TTGGAAGACTTTCACCAGACTAGACAGCTGCT CCCTACCCCAGGAATCCACGCA CCTCACCTCGCTCACATAATGCATATTCAAA CGGCTTGCAAGAAAAACCACCGG TGTTCAAAACAAATTTAGTGCAGGGTCCTACCC CAAGACTCATGTTCCGTCCAGTTAGCGAGA TCGGTATCCGAACTTCACCCGGG CATCTTAACTCCGTGGAAGAAGGTCCTTACGA CCATCTTATGGGCGGTTGACATTACCTCTAGA TGCGTGTCCCTCAACATGCGTACAG CCCAGCTGAAGCTCAGAAATCGTGCT AGATCCCTGCCCTAACGGCTGTGG CGCGGAAAATGCGCCCACA CGGATTTTACCTACTGGTCCCGTACTTCGG CCTCCCGACGGATGCGCG CGGACAGACTCAAGCACACACGGG TCCACCCTGCCCATTTCGTACGA CCCACAACAAACACACAAGGACCGG CCCCTGTCGTTTGGGTCCCCC CCTTATATGTGCACGGCAAATACTTCTACTGCAAC CCCGGCGCCTATCCACTCCC GATTAACCAAC ATTTGTCTGTA CCTCGAACACT TGTTACCCATG GTCCCTGTTTC CTACAAGCCGG CAGAGGACGGC ACGCATGCAAG AGACTCGGTGG ATCCGGTGCTG OR alternate MSC soln AGGTTGCACTG CTTTCACCAGA CTTATAATCCT ACCACTCAATT GGACTCCTGGA CCGTGCCCAGT CCCATAGCATA AGCCCACATGT TTGATGAAAGG GACTTGATTTG CATTCAGTATA AACTAATGTCA GTCCCTCAACA TCTACTTGAGA CCCTCCGCATA CCCACCCGCTT CAGATGGGACG TGACGACAAGA AACCGACAGAT GGGCCTGCGTA GACACCTGCTT CGGAACCACTT GTAAATGCCGC 1 1 HumanHerpes3 10335 19 1 19 19 19 19 19 19 HumanHerpes4 Epstein-barr 10376 4 1 4 4 4 4 4 HumanHerpes6 10368 3 1 3 3 3 3 HumanHerpes7 10372 1 1 1 1 1 1 Japanese encephalitis 11072 43 2 37 37 37 38 Mumps virus 11161 17 1 N N Newcastle diseasevirus 11176 38 4 17 16 16 321 131 14 1 Sendai virus 11191 13 1 13 group1_16 group1_1 group3_100 group3_1010 group3_1084 group3_1022 group3_1036 group3_1080 group1_101 group1_116 group1_266 group1_325 group1_425 group3_1017 group3_10508 group3_10819 group3_12257 group1_10 group1_105 group1_109 group1_24 group42_324 group42_461 group42_666 group248_605 group119_253 243 170 group174_256 group474_488 group559_542 group124_1000 group26_337 CTGAAAACGACGGACATGTTTCT GTAAATGCCGCCCCTTTG AAACGTACGCTCCTACTACCGAGTAT CTCGAATTTTTGTTGCGGTACATAG CAATGAGCGCGGACAGTTT GTGTTGGGAGACATGGGAACT AACTACATGGAATTTCAGAGTCAAAGG ACTCGCCACAACTCACAATTTAGA GGGCTTTGGGTTCCATTGT CGAACGATGAGGAACGTGAA TGCAATGCCCACCCACTA GTGGGCGCTCCTCACTTT CAAGTACAGAGCCCACCACAGAT ATACTCCGCCAGACTGGAACA AGCGTATAGTTATCGAGGGACACAT GCCGAATGTTTCCAGAAAAGA GGTGCATAAACGGGACTATGG ATACTGACGGGCCGCTCAT GTGAGACCGACATTAATGACACTGA AAGAGGTAAACACAGCTAACGAGACA ACAGCTGTAAGCTGCAGGAAAGA CCCAGGCGGCAAAGTTTAC GAGAGCGAGGTCATGAAACCA ACACTCGTCAGTGCTTTCCTCTCTA GCAGCTGTTCCAAGTGTTGTG GACGTCCCATCGAGGGATT GATTAACGGTTATAGGAGGAGCCATAA ACAGTTTGTTCTGCCTCACTCAAG TCTTTTCTACTCTGCGTTCCATCA ATATCTCGGGTCGAAGACTCAAGA CTCACTGAGTACCTACTGTCAGATGCT ATCACACACTGCGAGGAGTGTT CTTCCCATTAATGGACGTGAATC CGCGGTGCACACACCGGA CGCCGGGTATAAGGCAGCCCC AAAACGGTATGAAACGCTATTACCCGCCTT CCTTTAAATCTCGCGCCGCCTGA TCCATATGCAGTAAACGTAACCCCCAAGAAA CCACGACACCCGAGGTGGAAGC CGTAACATATTTTAACGCATCCCCGTGACC CGGCACCTCCGACGCTTCG CTTTCCTGGCCAACGTGAGGGTCC CACCGCCTTATGAGGACCCATATTGGG CCCGGCGGACCCGATCAG CCAAACCCATGTAAGTCATGTGTCAGAACG ACTGCGGCCCCGCTGGAC CTACAGACGCCGGAGAAATCCAAGACTTG CTGCGTTGCATAAAAACTTGGACTGCTAAAAATTAC TTACAATCGACCATCAAAATATAAAGAGCACAGCAC TCAAATAAGTCCCGAGAAAGACGTCAGAGCTATC CACGTCCGTTAAAACAACGCCACATG TGTCCTCTAGCTAATGCTTTGCTGCAACAAA AACTCGCCACTGAAAAACTTGGAACACACTT CACCTCTAAGCATAACCTGTCGGGCACA CCCTCAAACTTGGTGACTACGGAGAAGTCA CACTCCTTGGCTCACAGTCCAGTGTGA CAGCCACACACGGGTTGATGTGATACC CACCTGCCCACTCCCCCTTTGG AACACCTGATCCCATTGAATTGGTACATGG TGGCAATGCCCCCAAAAGCCT CGCCCATTGCTTGCTGCACG TGACACCCAAAATCGGAAGTCTTGCA CATATGTCACCACATGTGAAAGCAGCACTAAGG CCAGCCAACCTATATTACATGTCTAGGAAGAGCCTT CAGTTTCTGCAGTATTTGATTCCATTGCACG TGATTTCCGCTACTACCCTAATGTTGTGGCA GCGCAGACATC CTCTCTTGCCG GCCTCCCGGTG CACTCACGCAT CTCAGCCGTAT CAAAGTGAACA GTGGATTATTT CTCATGCATAT GGTTCAACTCC GAGTGACGGTC GCCAAGATAAT ACCAACAGGTG GTAACCGGTGG TTCGTTACGGT ATTCAGGCTAG TGTATTGTAGC ACGTCCAACGA ACCGCAGACTG CCACTTCCGCA ACCGGGAAACC TTTACGGCTGC AGTCCACTCCT TCAAACTTGGT ATTTGTTGTAG TGATGGACGTG GCTCACATTCA TCTGAATTATC CAAAACTTCCA ACAACCTAAGG AAGCCCAGATT CTCTGTCCTCT TGCTGCTAGAG AGCTTCCTGAT N St. Louis Encephalitis 11080 2 1 12 2 2 2 2 601 group17_83 group17_172 group17_233 group17_39 GAAAGGATCAGGCCGCATA TCGCTGACTCTACTGGCTGTTG TCATGATTCGGTAGATTCCTGGTT GTTTCGTAGGACTGCTCCTTCAGT GGGTTGAAGAGGATACTTGGAAGT CAGACTTTAGGGCACGTCTTGCAAACACA CCAGCGTGCAAGCCGATTCG TGACGGCACGTCCCACAATGC CATGATTCGATAGATTCCTGGTTTTGTCTCACA CGTGCGGTTCATACTAGCCATCCTGAC CATCCCGAGAC AGATGCCTCCT CTGGGCTTGAG CCGTCACCAAA CTGTAGAGCTG Papillomaviridae Human papillomavirus type 16 151340 333760 107 14 72 1 14 14 14 14 1879 1883 1886 1892 1981 1977 1982 group1_4 group1_13 group1_16 group5_11 group5_16 group5_41 group5_55 group5_67 group2_10 group2_6 group2_15 group33_79 group36_106 57 18 CCGTACCCTCTTCCCCATT ACACAATTCCTAGTGTGCCCATTAA TCCACTACAGCCTCTACATAGAACCA GACAATCACCTGGAGTTACTGCAA TTGGACAGAAACTACACTGCTGTTG TTGGACAGAAACTACACTGCTGTTG GTGTAGGCCTGCTGGACACA AACAGACAGGAATTGGCTCAGA GTCTTTGTCGACTGGGAGACATT TCGACTCCAAATGTTATGTCTGTATG CAGGACTTGGGATTATTGAGACCTA CCATTACATACTCACCACGAAATCTG TACATCCCAACTTTTGTCTCCATTAC TCTGAGGAACCTCTCCATTGCT GGGCACACCTGGGATTACA TAGCTGCTGAATGCTTCTATACATTCT CCCTCCAAGTCAGACTCCCTTTA GTCTCTTCAAGCTTTCTTTAGCTTCGT CCACCCCCTGTAATTCTAAAGC AACTTTATGATCCCAGTCAGCAAAA TATGAGTGGCCAAAGGAAATATAGGT AGAAACTACTTGGGCAATAGTCAATTC CCATTAACAGGTCTTCCAAAGTACGAATGTCTACGT CTACGTGTGTGCTTTGTACGCACAACCG CCATTACATCCCGTACCCTCTTCCCCAT TCCTTTGCCCCAGTGTTCCCCTATAGG CCCCAAACAATGGGTATTGCACGGT CGAACATAGTCAGCACAACTATATGCCCCAA CCCGCCCTAGTGGCTGCAGTTCTAA TCCTCTGGACCCACACGATTTCTGG CCTTGTCTCAGTCGGCTGGACCATG CGCACCATCCCCTCCTGAAAGG CCATTTGCACACTAGCTCATCTTGTTGTGTTAGA CCAGACCTATCCTTAAGTTCAGATCACGTTTTGTG CACGAAATCTGAATTACCAAGTTGCCAGACCTAT AGGCAACCATCTACACTTCTAACACAACAAGATGAG CACTCGAAGACTCTGACCTGATCTCCGAC TCCACCTAGAAATGCCCCTTTCGTCA TTCCCAGCCATATCATGACGAAAGGG CAGCATCACGTGCTACTGCTTGTCCTAGCT TGGCTTCCCTGCACCATTGTCATG AGCTACAGCCCCCGGAGCTCCAGTA TCCCTTTGGGCAACCTGCCTTACC CCCTCTATGGTAAGGCAGGTTGCCCAA CTTCGGTTGTG AACCGGACAGA GAAGACCTGTT CAATTGTGTTT Human papillomavirus type 71 120686 5 1 5 5 5 GTGTGCCTGGC TTACTCACCGT CCCTATACAAC Human parainfluenza virus 1 12730 1 1 1 1 1 GGTTCCCCTAC AGATTCGATCC CAAAAGAGAGA Human parainfluenza virus 2 11212 5 1 5 5 5 5 5 TCTGAGGAACC GGGATTCAGAT ACACAAAGCGT CAGGACTTGGG AGCCAGTCTCC Human parainfluenza virus 3 11216 2 1 2 2 2 ATATCCCTCTT TTGACGTCTGC AATAGAGCCAT JC polyomavirus 10632 380 2 N N 296 369 376 379 TGTGCACTCTA GGCTATAGCTG GATTGTCTCCA GTGTATGAGTG BK polyomavirus 10629 120 1 120 120 120 group5_102 group5_1089 group5_1275 group2_4 group2_6 group2_3 group29_212 group29_1218 group29_465 group29_916 group72_200 group72_205 group101_1107 group117_485 group170_846 group5_431 group20_190 group11_115 group47_451 group65_1141 group96_1039 822 674 685 group1_1226 group1_1434 group1_3268 group20_3871 19 276 467 334 CAATACCTTGATCCTAGGCATTGG GATTTTCAGTGGCTGAAATTGCT AGATGGCCCCAACCAAAAG ATGTTGGTGTACCCACAACCAGTA GCAAGGGCCCTGTTTCTTC CTTGTAAAGTTACAGTTGCAGGCAAA CAAAGTCAGCAGTCTACGTCAGGTA GCTAGGCCTTGTGGCGTTT GCTCTGTTTGGAACGCAACA GGTTGGGATCACATGCAATC GCCTACACACCTTGGGCAAT ACACTCCAAAGGCGATATGGA ATCCGTTTGGCATGTTAATGTTG GAGCCTTTAGATCGCTCTTTGG GGCACAAACCAGACCGTCTT GGAGTGATCGAGAGTGAGCTCAT GCTCACAGACCTCTGGAGGAA GAAAGGTTACACTTTGGGCAGAGA GGCTCCAGTCGGTGAACAT TTCAGGGAGACTGTCCACCTCTA AAGTTTCTCTCAACCCTCTGGAGTAG CCGGAAACTCGAAGATCTGAGA CAACTCAGAGATCCACGGGATTA AACATATGTTGAAGTGCCTCAGGAT GAAGAAATAAATGATCAGACGAACGA CATGTAAATGCTGGTAAATCAACCA ACTTAGTCCTTACAATAGGTCCTGCAA TGCTTTACCATAACCTTTATGAAAACA CATTCCATGGAGCTAAGGAGGTT CTGCTCACAAGTGGCACACA GTCTATGAGACCGATGCTGTGAGT TTCACTTGATCCCGCCATCT TTGCTACTATTTCCCAGGCTTTGTGGCA CCTTGCTACTGTAGAGGGCATAACAAGTACCTCAGA CCCGTGCAAGTGCCAAAACTACTAATAAAAGGAG CATTTGCCTGCAACTGTAACTTTACAAGCCA CATAGTAACCTCTGTAACCTGCAGTTGCCCACT CATAGTAACCTCTGTAACCTGCAGTTGCCCACT CCACTCAAGACGCAGTCGGAGGTCA CGGTCCATCCAAGCCTCCACATCAT CGGACTCTGCCACATCATGCGTG AGGCTAGAGCCAAGCATAACAGACTTGCTCCT CACCATCACCCAAGGAGTACAAGAAGGGT CCTTGTAAGAAACCCCCTTTCACGCAACT TGATTCTAGCCTCCGTCCAGTGAGCG AACGCCCGTGACAGGTCAATTGCTA CCAGAGTTCCACGCTCTGTCGGGTATC CCAGTTACTTTGGCCGGTCCAAAGAGC CACTCCGGTCTTTCCCTGGCGTC ATTGTGACCTTCAAGGATAAGACTGACATCCACA TCCATCCCAAGCTTTGGACATTCATAGG CGCACTTGGATTGACAAAGATCTTGCTCA CCTCTCGCTCATAGCGTAGCACGTGTTG CCATGTCTGTGCATAAAGCATCAATGGC CAGTTCCTCACCCTTCTGAGATGTTGGG AGCCACTTTAGACAGAGTTCCCCTCTGTAACTCA CACATTAGTAGTAGCAAGTGCAGGACCTACATCTGC TGTAAGGCCAGAAGCACACCAGTCACAC CCAAAAATTTCATCATGCCTAAGAAGGCTGATAAA CCTCTCCCCAATCTTTTTCAAAAATACCTTTTGA CTCAACCGGTGCACTTGCCAGC AGGCCAAAAGCCACTTCCGTAGTCACC CAATCTGCTCACAAGTGGCACACACTAGG CGATGCTGCGAATCTGCAATCTGCT AAATCTTTCTG GAGCACCAGCA CTCTGTTATAG WU polyomavirus 440266 6 1 6 6 6 TATGTTAATAT GGTGTTTAATA TGTTTAATAAG West Nile virus 11082 84 6 74 74 74 74 6 6 1 1 1 1 CCATCCAAGCC GATGTGGAAGT TCCCAAGGTGC GCAGCTTGATC TCTGTAAACGC AGTGGACGATG ATGAGTACTGC TTCCTCCCACA CTCCAGGTACC GCCTGGCCTCT Yellow fever virus 11089 15 3 12 2 1 AGGGAACAAAT TTCACACTTGG TGGCAGAGATG Rabies virus 11292 26 2 24 22 N N N 22 24 21 7 7 7 8 AAAAACTAACA CAACCACTATG ATTTGACCCAA TTGCTCCACAA AGAATCTTTTC Human respiratory syncytial virus 11250 9 2 CTTAAACCAAC TTTATACCACT GGGTAACAAAG ATTTAGCTGGA Influenza A MP Segment 11320 3964 ~50 N N N N 352 337 342 283 TGCTCACAAGT AGCTACTCAAC CTAAGGAGGTT TGGCCTAGTGT Influenza B MP Segment 11520 237 4 200 4 211 150 group1_29 group3_38 group16_15 group23_36 1266 1431 1879 1881 334 4290 4758 4269 256 47 897 group55_520 group76_813 group235_972 group246_124 group469_481 group483_702 group43_592 group91_781 group135_993 group287_636 group387_891 group486_1034 group520_54 4656 6651 1574 2467 AGGCCTGATTCTAGCTGAGAGAAA TGCGAGTGCGATGCTTGT TAGCTGAGAGAAAAATGAGAAGATGTG GCACAGAGCGTTCCTAGTTTTACTT TGCTTATGTCTCTGTAGTGTCTTCACA AGGATGGTTACAGGACTAAGGAACA TCCCCAAGGCAAGTTCATG CCAAGATATGCCTTCGCAATG CAGAGGTTTGTTTGGAGCCATT GCGAAATACCCTGGGTAACATG GAAGACTACTGTTCAAGGCACCATAA CAAATGTCTAGAAACCCATCATCAAC CTTTCGCACTGAGTAGAGGCTTT GGTGTTTTGAATTCTACCACAAGTGT AAGGTGAACTCTGTTATCGAGAAAATG GACTCCTCTTCATACTTGGGATAATCA GACTCCTCTTCATACTTGGGATAATCA TTTTCTTTCTCCATTATGTAGGACCAT TTTTGAGAGCACTGGTAATTTAATTGC TTCTTTGTCAGCCAGACCATGT GAGTTCGGCATTATATGTCCATACATC TGATAATCATATGCAGATCCTGCATT ATCCATACCAACCATCAACCATT AAACCCCCATATTGCTCAATTTC AGTTACTGAATTCTTTCCCAACAGCTT TGCATTCTGACTTTGTCGTACAGAT TCTCAAAATTTATGGTGTCCCACAT GGGTTATACCATGGACAAACAAACA TTGATGCCTGAAACCATACCAA ACGTATTTCTCGAGGTCCTGAATT GACTCAGAAATGAACAAACTGTTTGAA GGGTCAATCAGAAATGGAACTTATG TCATGGTCATGTACCTGAACCCTGGAAATT CTCGCATAAAGCACAGAGCGTTCCTAGTTTTACT TCTCATGGTCATGTACCTGAATCCTGGAAATT CCAGGATTCAGGTACATGACCATGAGACAATACA CTACTACTGGACTCTGCTGGAACCCGGG CCATCCATTCAATCCAGAGGTTTGTTTGG CCCTTATGCTGGAGCAAACAGCTTCTATAGAAATTT TCACAATTGGAGAATGTCCAAAATACGTCAAAA CACAAAATGCCATTAACGGGATTACAAACAAGGT CGGCAACGCTGCAATTACCCAATTGTA TGGTGCTATTAAGTTCCCAGTTGCCTCAAA CACCTTGTTTGTAATCCCGTTAATGGCATTTTG CACCCAGTCACAATAGGAGAGTGTCCAAAGTATGTC TCTATCAGATTCTGGCGATCTACTCAACTGTCG CTCAATTCACAGCTGTGGGTAAAGAATTCAACAAAT TGCATTGTCTCTCAGTTGCATTCTGACTTTATCAT CGCATTGTCCCTCAGTTGCATTCTGACTTTAT CAATCCCCTAGTTCAAGTGGAGGGATTCC CATTGCCTTTTCACAACATTCACCCATTG CTTTCTCGAAATGTGTCACGCTGCTGA ACTTTGTTAGTTATCCCATCAATTGCCTTTTGAGTG CCCAGCTATCATGATTGCCAATGACAGG CAATCCTGTTGCTAAGACCAATCTTTCCGATTTT CCTGACACTATTCATGCATTCATCATCACATTTATG TCTGCTGCATACCCTGATCCCTGGTC CCATCAAAACTAGGAGTTCGGCATTATATGTCCAT TCGACCTTTTGTTCAATGTTGATGTGCCTAC TGCCAACAATTCCACAGAAAAAGTCGACA TGCTTGACATATTTGGGACATGCCCC TGCTTGTCCTGTGCCCTCAGAATTTTGA ACCACAAATGTGACAATGCCTGCATAGG TGGATCCTATGGATTTCCTTTGCCATATCATG GCGTTCCTAGT CCTAAACCCTG GCGTTCCTAGT AGCTGAGAGAA H1 Influenza A HA Segment multiple nodes 634 19 N N N N N N N N N N N 388 388 31 66 448 392 8 421 300 216 374 19 16 57 26 44 29 AAAGCCTCTAC CCTTGTTTGTA GGATGGTGAAT CCTGTAGCCAT CAGCTGTGAAT GTCAACCTACT TATTATTGGAC GAATGAGCAAG GTTCCTTAGTC GGAGACTAAAA TTCTTCACATT H2 Influenza A HA Segment multiple nodes 106 6 GTTCTAATGGA GTTCTAATGGA CAATTCTAGAG TTACATATTTG TTGTGTTATCC CAGGATATGCA OR Alternate MSC soln with shorter amplicons. 7 13 2 31 52 27 38 14 H3 Influenza A HA segment multiple nodes 1590 23 N N N N 227 216 466 408 GATCAAAGGAG CATAGGTGAGT AAGGAAATAGG TGGTATGGATA AAATAAAAAGA CTGTACCAGAA GTGACGTTTCG ATGACAAGCCC ATAGACGGTTG AGCTCAACACC TTTTTGGCAGG N N N N N N N N N N H5 Influenza A HA segment multiple nodes 1137 6 408 393 357 413 254 255 350 237 476 60 359 394 326 18 345 380 5741 3928 6138 3162 3722 3895 4159 1934 5250 1416 group6_61 group34_81 group39_85 group48_114 group110_66 group111_67 group4_80694 group6_17063 group8_11422 group8_15194 group8_66420 group13_32917 group14_2030 group21_12566 group22_75711 group23_47661 group27_16329 group29_17149 group37_40960 CCTCAGAATTTTGATGCCTGAAA TGAAATGGTTTGTCATTGGGAAT TGATGCCTGAAACCGTACCA GTTACTTCAAAATACGAAGTGGGAAAA AATGCAAATGTTGCACCTAATGTT TCAAATGCAAATGTTGCACCTA ATTCCCTCCCAACCATTTTCTAT TGAAGACTATCATTGCTTTGAGCTACA CTGAGCGACTCCAGTCCAATT AATTCTGAGGGCACAGGACAA ATGTAAGACCATTCCGGCACAT CATTTTCCATGAGAACCAGAAGTTC AAGTCCAGACATCTAGAAATCCGTCTT CAGTGTAGCTGGGTGGCTTCTT ATGTAAGACCATTCCGGCACAT CCGTTTCTTACACTTTCCATACATTC GTCTATTATTCTTTCCCCTGCACTGT AGTGAGAAGCAGTGTGTGCTCAT CAGCGGCAGCAGCTGATA AGAAATCACTCTTGGAATTGGATCA CAAGTCTCATTCCAAGGCACAGT CCTGGTATCTAGAGATCCCTCAGATC CTGACGGTACAGGCCAGACA TCCAGTCAGACCTCAGGTACCTTT CACCTGCCATCTGTTTTCCAT ACCTGCCATCTGTTTTCCATAATC CTGTACCAGTAAAATTAAAGCCAGGAA GACTCTGGTAACTAGAGATCCCTCAGA GCTATGTCACTTCCCCTTGGTT CCTGTTGCCAATTTCAGAGTGTTTTGCTTAACATA CCCGAGGAGCAATTAGATTCCCTGTGC CCTGTTGCCAATTTCAGAGTGTTTTGCTTAACATAT CCCAATGACAAACCATTTCAAAATGTAAACAGG TCAACACCTTTGATCTGAAACCGGTTGTTT CAACACCTTTGATCTGGAACCGGTTGTT CCCCATATGTGATCCTGTTTACATTTTGAAATGG CAAACGGAACGCTAGTGAAAACAATCACG AGGTCCCATTCCTTATTTTGGAAGCCATCAC AGAAATTCCATCAAATCGAAAAGGAATTCTCAGAA CTTCCCGTTGTGTGTCTTTTCCAGTATGTCTTG CTGCCTCAAACTGAGTGTTCATTTTGTCAATGATT CGGCCTCAAACTGAGTGTTCATTTTGTCAAT CCTGTGTTACCCTGGAAACTTCGACAATTATGA CTTCCCATTGTGTGTCTTTTCCAGTATGTCTTGG CCCTAAGCTGTAGTCGAACCTTGTCGTAAAGGTTC CCCCTTTTCTTTTAAAATTGTGAATGAATACTGCCA TCCGACGCAACGGGCTCG CGCTGACACCCAGAACTTTAAATGCTTGG AGCAAGAGTTAGGCAGGGATATTCTCCCCTCTC AGCATATAGTTTTTCCTGAGCAGCCCCATAGAC TCCGACGCAACGGGCTCG CAGCTCCAGGCAAGAGTCCTGGCT CACAAGGCTACTTCCCTGATTGGCAGAA TGGTCCTTTCCAAATAGGGTCTCTGCTGTC TCCTTTCCAAATAGGGTCTCTGCTGTCTCTGT CCCAAAAGTTAAACAATGGCCATTGACAGA CTCTAGCAGTGGCGCCCGAACAG TGCATGGCTGCTTGATGTCCCC TCAAAATGTAA GGACAATAGTA ATGACAAACCA GCATCCCTGTT CCATGATGTAT CCATGATGTAT GAATGCATCAC TACCTGTTGAG ATGCTCTATTG AACGTATTTCT CAGAGCAGGTT AGAATCCACTC GAGTGGATACG ATCTGAACTCT CAGAGCAGGTT TGGACTTATAA HIV 1 11676 1107 11 207 15 3 3 3 18 191 222 309 8 213 364 252 CAGGAATTTGG TGTGAGTTCCT GGGTGTTGCCC TGTTGGGATAA AGATACCTTAG CCACCGCCAGC TTCCAGAGCAG CCCTGGCCCTG AAATTCAAAAT TTTAAAAATTC TGTATGGATTT CGAGTCCTGCG AGAAGGAGCCA Bacteria Haemophilus influenzae 727 15 1 15 15 15 group3_1204 group3_103 group3_5670 CCATGGAAACTGACCCAATAGATA CAGGCTTTGAGCGTTTAAATAAATATG ATCTTGTTTGGGTTCGCAAAAA TGCAACAGCAAGCCCAGCACG TCCTCGCAATGCAGCGGCAG CACCGCCACGAGTAACGAGTACATTTTCAG TGTAAAAGAAA GGATCAAGCTG GAATTATGCGG 15 15 Mycobacterium tuberculosis 1773 8 1 8 8 8 8 Staphylococcus aureus 1280 12 1 12 12 12 12 12 12 Ehrlichia genus 943 6 3 1 1 2 2 3 3 Ehrlichia chaffeensis Ehrlichia ruminantium Chlamydia trachomatis 945 2 1 2 2 779 813 3 6 1 1 3 6 6 6 6 Pseudomonas aeruginosa 287 7 1 7 7 group3_181 group3_1135 group4_1 group4_2 group4_9 group4_10 group6_100 group6_12 group6_112 group6_42 group6_161 group6_163 group1_95 group1_218 group3_121 group3_100 group7_25 group7_272 group1_12 group1_15 group4_45 group2_1027 group2_102 group2_1069 group2_1148 group27_1068 group27_1577 GGACATCAGCCCAGCCTTATTA CTCTTGGCGGTGCGTTACT GTTGTATGCGCACGTCCTTT CGGACTATAGATCTCACGCAATATAGC CCACACACCAGGAGCCAGTA GGAATCGAGGTGCTTGTCATC CCTTACATTGATGCTGAGCGTTT TGTTGGAGGATTACGCCCTTT CCATATGCACGTGGTTCCTTAC AGGTATCGACAATACTTATCGGAGACA TGAATTTTGCGAAACCAGTAATAAGT GTATTAAAGTAACCTGCGCCTATTGTG CAGGGTACCATTGTCTTTCAGGTT TACTACAGTGCACATGACCCTATATCG CATCCGAGGTTCTCTTATCTCACTAA CTTGTGTAACTTCTGATACCTCCTGAA AATCTACATGCGCATAATGCCTATT TACATCGTGAACATGACTTTCACGTA ACTGCAGATGCACCTGGTATAGG CATCCGAGGTTCTCTTATCTCACTAAA ACCACATAAGATACCCATTACGTATCC CCAAAGACATAGTCTTGGGATGAC ATTCATGTCTTTCTCGAATCTTTTCA GATACTGCTCATCCCAACGAACTA TACTCATGTCCTTCCCTCTCCTCTT ATAGTGCTTCAAATAGCCATCACTTG TTCCCCTGTGGTTGGCTTT TCACCTTTAGCTGCTTTAAATGCTTCAGCCA TTTTGTTTCCGCGTGCCTTTGCTAAAT TTTCGCACCGCTCCGATACCG CGATCATTTCCACGAGCTACGATGCTC CGCTCACAACTCGCAGCGTAGTTTGA CCTCTCGGATCGTTATCGCATGCC CCCTAACTCCCCACAAATCTGGAACGATACT AATCTTACGGCCTTCAACAACTAGCTCATACCAA TTCGTACTCTTGGTGCGCATAGTCCATTTT CCAGTAACACTAATTCCGGATACGGCAACAAATA TGCGCCTAGCGTCGTACCACGA CACCACTGTTACTTACTGATGCAACTAATTTCGGTG CCCTGCAAAACTGCTTGCATAAGTAGGGTC CCATCTGGCCAATCTAATAAATCCAGTGCA ACGTGCAATACGCCTAACACGTCTTTCC CCACTGCGTTTAGTCGTACCCTTGACTAATTGC CATACTCTACATGTGCTGTTGAAATGGTAATCCCTC CATTGCAGATCTTAACCCACCAATTAACTGGTGT AGGTTTACTTCCTTCTGTCTGCGACGCTAATGTA ACGTGCAATACGCCTAACACGTCTTTCC AGCTAAGACATTTGCGTTAACAATACCTGCGAAATT CCGGAAGGAGCTACCAGCCCACTT CGCTCTCTTCCCTTTAGGAAGCCGACA CGGCATGCTGAGTCTTCTCAATACGATTTACTACA CGGACACCTACCTAGAAATTGCCCACACTC CGGAGCGTTCACGCCCCA CCAATTGATCCCACTTTTACCCACTTCATACC CAAGAAGATAT CAAGCCACAAA CATGCCACGTT CTTGCTGGCTG GCTCGCTAACC GTACCCGGAAG ACATCCAATAT TCAGTGTGTTT CCTTTAGCAAT GGTGTAGAAGT GTCGGCGGTGG TCTATATAAGG AATACTCACAG GCTAGTGCAAA ACCATTTTATG AGAACTAGAAT GAAGAGATTAA TTGAAAGGTCC AACCTTATTCT ACCATTTTATG TTATCAACACT AGATCGAGTTA AGCGCAGTAGC TGCAACGTGTC AGTGAGGGTGA TCAGTCATCAC AGTGTGGATTT 7 7 7 7 Escherichia coli 562 42 1 42 group27_184 group27_2042 group27_2246 group27_4009 1 TTTTTCCCGGGCCTAACC TCCCATGACAGTCCCTCCTT GGGACGCCGGTCTACTCTT CTCCGATAAGAATAATTCGCAACTC TTATCTGCTTAGCGTGCTGGAA TCCTATCTGTTTCGTGGCCAAGTGCC CGCATGTATTGCGCCTGCCATG TTGTCAGGTCGCCCGATTCTCCTTC TTGCTTTCTATCCCCGTTTGTTTCCCA TCTGTTATCGCCTCCGCTGTCGG GAGTGTTTTCA TGAACCCAAGG GACAGGCCCCT CGCTAACCAAG CGCCCGACATA OR Alternate MSC soln with shorter amplicons. 2 37 16 N N N N N Neisseria meningitidis 487 3 1 35 34 35 35 32 3 3 3 3 3 group6_1790 group11_1327 573 1762 1454 33 454 group3_120 group3_36 group3_33 group3_39 group3_48 CGCATGTCGTTACGCCATAA CAATACTTTGAAACCCACAGCTGTA GTAACGACAATGGGCGAATTACT GTAACACCCACGGAGGTAATACATC GGCTTACTGAACAAATATCCCCTTT GTAACGACAATGGGCGAATTACT GCCTCCGGGCGATAAACT CCCACCGCACCCATAGAC GGACAAGTGACTGTTCAGTCCTATTT TGCGGTACAAGGATGATGTTG GGCCTATGATGGCGATGTC GGGAAGATTTCCTCATGGTACTTC CAATCACCACAGATGGAACAGGTACGGC TTTCAGACCAGCACGTGAACGTATCTTCA CGCCTCGATTATGTTCTTTGCGCC TCTGGCACCAGTGGTTACAGTTCTCTTAATTATCGT CGATATATAAAAATCGATCGTCCACATGCAGAGA CGCCTCGATTATGTTCTTTGCGCC TGGGCCTTCCGGATCCACAACA CCAAGGCAACAGTTCGTACTACATTGCCA CGGACAGATTGTATGCCTACCAATCCGG CTTCCGTGTCAGGATGTCTGCCTGATACA TGCTCAAATCTATTTCAAACGGTGCGTAACGT ACATCGGATCCGCCGTCCAAAC GAGCGGGCATA ACCTTTGAGTG GCTGAGGTGGC GCTGTCACCAC GCACGATTGCA GCTGAGGTGGC GCTTACGTCTA AACGGCAAATG GCCCAATCCGC TGAACGCATAC GCAACGTATAC GAGCAGATTCC 3 group3_88 ATGTACCTTAGCCGTTCGGCTAT CATGCGTTCTCAAAGCTGAACGCG No signatures are predicted to have any false positives, except for two of the Newcastle disease virus signatures indicated with 1, which are predicted to detect Goose paramyxovirus. Goose paramyxovirus is not currently classified under the same taxonomy node as Newcastle disease virus and pigeon paramyxovirus. GAATCTTTCAA