Mercurial > repos > jpayne > seqsero_v2
view output/forward_25k.fastq.gz.bam @ 12:4ac593d4b40f
planemo upload
| author | jpayne |
|---|---|
| date | Wed, 14 Aug 2019 17:45:41 -0400 |
| parents | fae43708974d |
| children |
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SN:fljB_z_Salmonella.enterica_IIIb.61:i:z_AY353335_k,z__1500 LN:1500 @SQ SN:fljB_z_Salmonella.enterica_IIIb.48:i:z_AY353336_k,z__1500 LN:1500 @SQ SN:fljB_z_Salmonella.enterica_IIIb.50:k:z_AY353337_k,z__1500 LN:1500 @SQ SN:fljB_z_Salmonella.enterica_IIIb.53:z:1,5,7_AY353338_k,z__1500 LN:1500 @SQ SN:fljB_z_Salmonella.enterica_IIIb.48:z:1,5,7_AY353339_k,z__1500 LN:1500 @SQ SN:fljB_z35_Salmonella.enterica_Tamilnadu_AY353340_other.z35__1488 LN:1488 @SQ SN:fljB_z35_Salmonella.enterica_Kolar_AY353341_other.z35__1488 LN:1488 @SQ SN:fljB_z35_Salmonella.enterica_III.b.65:z52:z35_AY353342_other.z35__1488 LN:1488 @SQ SN:fljB_z35_Salmonella.enterica_IIIb.35:z52:z35_AY353343_other.z35__1488 LN:1488 @SQ SN:fljB_z35_Salmonella.enterica_IIIb.38:z35:z52_AY353344_other.z35__1488 LN:1488 @SQ SN:fljB_z39_Salmonella.enterica_II.43:d:z39_AY353345_other.z39__1500 LN:1500 @SQ SN:fljB_z39_Salmonella.enterica_II.4,12:g,m,t:z39_AY353346_other.z39__1500 LN:1500 @SQ SN:fljB_z39_Salmonella.enterica_II.52:z39:1,5,7_AY353347_other.z39__1500 LN:1500 @SQ SN:fljB_z39_Salmonella.enterica_II.51:l,z28:z39_AY353348_other.z39__1500 LN:1500 @SQ SN:fljB_z39_Salmonella.enterica_II.6,7:z39:1,5,7_AY353349_other.z39__1500 LN:1500 @SQ SN:fljB_z39_Salmonella.enterica_IIIb.40:z39:1,6_AY353350_other.z39__1500 LN:1500 @SQ SN:fljB_z6_Salmonella.enterica_Bere_AY353352_k,z__1503 LN:1503 @SQ SN:fljB_z6_Salmonella.enterica_Weltevreden_AY353353_k,z__1503 LN:1503 @SQ SN:fljB_1,6_Salmonella.enterica_Poona_AY353355_1__1521 LN:1521 @SQ SN:fljB_1,6_Anatumstr_AOZZ01000116_1__1511 LN:1511 @SQ SN:fljB_1,6_Anatumstr_APAA01000114_1__1511 LN:1511 @SQ SN:fljB_1,5_Bareillystr_AOZP01000315_1__1511 LN:1511 @SQ SN:fljB_e,n,z15_Braenderupstr_AOZM01000055_e__1496 LN:1496 @SQ SN:fljB_e,n,x_Chesterstr_AOZI01000020_e__1496 LN:1496 @SQ SN:fljB_1,7_Gaminarastr_AOZF01000073_1__1511 LN:1511 @SQ SN:fljB_1,7_Givestr_AOZG01000012_1__1511 LN:1511 @SQ SN:fljB_e,n,x_Hadarstr_ARYR01000012_e__1496 LN:1496 @SQ SN:fljB_e,n,x_Hadarstr_AOZE01000017_e__1496 LN:1496 @SQ SN:fljB_e,n,x_Hadarstr_ABFG01000005_e__1496 LN:1496 @SQ SN:fljB_1,2_Heidelbergstr_AMMX01000009_1__1511 LN:1511 @SQ SN:fljB_1,2_Heidelbergstr_AMBU01000011_1__1511 LN:1511 @SQ SN:fljB_1,2_Heidelbergstr_AMBV01000028_1__1511 LN:1511 @SQ SN:fljB_1,2_Heidelbergstr_AMBW01000031_1__1511 LN:1511 @SQ SN:fljB_1,2_Heidelbergstr_AMBX01000038_1__1511 LN:1511 @SQ SN:fljB_1,2_Heidelbergstr_AMLT01000029_1__1511 LN:1511 @SQ SN:fljB_1,2_Heidelbergstr_ABEL01000015_1__1511 LN:1511 @SQ SN:fljB_1,7_Indianastr_AOZC01000015_1__1511 LN:1511 @SQ SN:fljB_1,5_Infantisstr_ASRF01000034_1__1511 LN:1511 @SQ SN:fljB_1,5_Infantisstr_ATHK01000001_1__1511 LN:1511 @SQ SN:fljB_1,5_Infantisstr_AFYI01000002_1__1511 LN:1511 @SQ SN:fljB_1,6_Invernessstr_AOZD01000029_1__1511 LN:1511 @SQ SN:fljB_z6_Kentuckystr_AYDR01000034_k,z__1493 LN:1493 @SQ SN:fljB_z6_Kentuckystr_AUQF01000002_k,z__1493 LN:1493 @SQ SN:fljB_z6_Kentuckystr_AUQJ01000001_k,z__1493 LN:1493 @SQ SN:fljB_z6_Kentuckystr_AUQH01000001_k,z__1493 LN:1493 @SQ SN:fljB_z6_Kentuckystr_AHUU01000123_k,z__1493 LN:1493 @SQ SN:fljB_z6_Kentuckystr_AOYZ01000091_k,z__1493 LN:1493 @SQ SN:fljB_z6_Kentuckystr_AOYY01000105_k,z__1493 LN:1493 @SQ SN:fljB_z6_Kentuckystr_ABAK02000001_k,z__1493 LN:1493 @SQ SN:fljB_z6_Kentuckystr_AUQI01000001_k,z__1493 LN:1493 @SQ SN:fljB_1,2_Litchfieldstr_APAN01000023_1__1511 LN:1511 @SQ SN:fljB_1,5_Manhattanstr_CBKW010000016_1__1511 LN:1511 @SQ SN:fljB_e,n,z15_Mbandakastr_AMRS01000032_e__1496 LN:1496 @SQ SN:fljB_e,n,x_Minnesotastr_AOYO01000082_e__1496 LN:1496 @SQ SN:fljB_1,2_Muenchenstr_ARYX01000100_1__1511 LN:1511 @SQ SN:fljB_1,2_Muenchenstr_ARYW01000037_1__1511 LN:1511 @SQ SN:fljB_1,2_Muenchenstr_AOXN01000021_1__1511 LN:1511 @SQ SN:fljB_1,2_Muenchenstr_AOYT01000042_1__1511 LN:1511 @SQ SN:fljB_1,2_Newportstr_AUQQ01000002_1__1511 LN:1511 @SQ SN:fljB_1,2_Newportstr_AUQP01000016_1__1511 LN:1511 @SQ SN:fljB_1,2_Newportstr_AYDM01000071_1__1511 LN:1511 @SQ SN:fljB_1,2_Newportstr_AHUB01000037_1__1511 LN:1511 @SQ SN:fljB_1,2_Newportstr_AHTP01000026_1__1511 LN:1511 @SQ SN:fljB_1,2_Newportstr_AHTQ01000031_1__1511 LN:1511 @SQ SN:fljB_1,2_Newportstr_AHUE01000047_1__1511 LN:1511 @SQ SN:fljB_1,2_Newportstr_AHUF01000051_1__1511 LN:1511 @SQ SN:fljB_1,2_Newportstr_AHTR01000013_1__1511 LN:1511 @SQ SN:fljB_1,2_Newportstr_AHUD01000057_1__1511 LN:1511 @SQ SN:fljB_1,2_Newportstr_AHTV01000035_1__1511 LN:1511 @SQ SN:fljB_1,2_Newportstr_AHTL01000056_1__1511 LN:1511 @SQ SN:fljB_1,2_Newportstr_AHTT01000014_1__1511 LN:1511 @SQ SN:fljB_1,2_Newportstr_AHUA01000025_1__1511 LN:1511 @SQ SN:fljB_1,2_Newportstr_AHTW01000052_1__1511 LN:1511 @SQ SN:fljB_1,2_Newportstr_AHTU01000008_1__1511 LN:1511 @SQ SN:fljB_1,2_Newportstr_AHTM01000016_1__1511 LN:1511 @SQ SN:fljB_1,2_Newportstr_AHTJ01000021_1__1511 LN:1511 @SQ SN:fljB_1,2_Newportstr_AHTN01000022_1__1511 LN:1511 @SQ SN:fljB_1,2_Newportstr_AHTK01000007_1__1511 LN:1511 @SQ SN:fljB_1,2_Newportstr_AHUC01000029_1__1511 LN:1511 @SQ SN:fljB_1,2_Newportstr_AHTZ01000054_1__1511 LN:1511 @SQ SN:fljB_1,2_Newportstr_AHTY01000074_1__1511 LN:1511 @SQ SN:fljB_1,2_Newportstr_AOGH01000019_1__1511 LN:1511 @SQ SN:fljB_1,2_Newportstr_AJMO01000050_1__1511 LN:1511 @SQ SN:fljB_1,2_Newportstr_AYEB01000020_1__1511 LN:1511 @SQ SN:fljB_1,2_Newportstr_AYEA01000014_1__1511 LN:1511 @SQ SN:fljB_1,2_Newportstr_AYDZ01000021_1__1510 LN:1510 @SQ SN:fljB_1,2_Newportstr_AYDY01000005_1__1511 LN:1511 @SQ SN:fljB_1,2_Newportstr_ABEW01000002_1__1511 LN:1511 @SQ SN:fljB_1,2_Newportstr_AYEI01000024_1__1511 LN:1511 @SQ SN:fljB_1,2_Newportstr_AYEH01000009_1__1511 LN:1511 @SQ SN:fljB_1,2_Newportstr_AYEG01000094_1__1511 LN:1511 @SQ SN:fljB_1,2_Newportstr_AYED01000019_1__1511 LN:1511 @SQ SN:fljB_1,2_Newportstr_AYEC01000044_1__1511 LN:1511 @SQ SN:fljB_1,5_Panamastr_AOYJ01000008_1__1511 LN:1511 @SQ SN:fljB_1,7_Pomonastr_AHIA01000072_1__1511 LN:1511 @SQ SN:fljB_e,n,x_Rubislawstr_AOYA01000090_e__1496 LN:1496 @SQ SN:fljB_1,2_Saintpaulstr_AYDS01000021_1__1511 LN:1511 @SQ SN:fljB_1,2_Saintpaulstr_ABAM02000001_1__1511 LN:1511 @SQ SN:fljB_1,2_Saintpaulstr_AOXF01000050_1__1511 LN:1511 @SQ SN:fljB_z6_Sloterdijkstr_AOXT01000012_k,z__1493 LN:1493 @SQ SN:fljB_1,2_Stanleystr_ARYV01000056_1__1511 LN:1511 @SQ SN:fljB_1,2_Stanleystr_AOXV01000001_1__1511 LN:1511 @SQ SN:fljB_1,2_Typhimuriumstr_AUQT01000077_1__1511 LN:1511 @SQ SN:fljB_1,2_Typhimuriumstr_AUQU01000007_1__1511 LN:1511 @SQ SN:fljB_1,2_Typhimuriumstr_AUQV01000001_1__1511 LN:1511 @SQ SN:fljB_1,2_Typhimuriumstr_AOXC01000008_1__1511 LN:1511 @SQ SN:fljB_1,2_Typhimuriumstr_AHUV01000080_1__1511 LN:1511 @SQ SN:fljB_1,2_Typhimuriumstr_AUQM01000018_1__1511 LN:1511 @SQ SN:fljB_1,2_Typhimuriumstr_AUQO01000019_1__1511 LN:1511 @SQ SN:fljB_1,2_Typhimuriumstr_AUQN01000019_1__1511 LN:1511 @SQ SN:fljB_1,2_Typhimuriumstr_AUQL01000023_1__1511 LN:1511 @SQ SN:fljB_1,2_Typhimuriumstr_AHVA01000007_1__1511 LN:1511 @SQ SN:fljB_1,2_Typhimuriumstr_AHUZ01000007_1__1511 LN:1511 @SQ SN:fljB_1,2_Typhimuriumstr_AOXO01000107_1__1511 LN:1511 @SQ SN:fljB_1,2_Typhimuriumstr_AJTU01000003_1__1511 LN:1511 @SQ SN:fljB_1,2_Typhimuriumstr_AOXD01000102_1__1511 LN:1511 @SQ SN:fljB_1,2_Typhimuriumstr_AMEE02000100_1__1511 LN:1511 @SQ SN:fljB_1,2_Typhimuriumstr_ATWR01000017_1__1511 LN:1511 @SQ SN:fljB_1,2_Typhimuriumstr_AMDZ02000041_1__1511 LN:1511 @SQ SN:fljB_1,2_Typhimuriumstr_AMEA02000051_1__1511 LN:1511 @SQ SN:fljB_1,2_Typhimuriumstr_AERV01000016_1__1511 LN:1511 @SQ SN:fljB_z6_Weltevredenstr_ABFF01000037_k,z__1493 LN:1493 @SQ SN:fljB_z53_IIIb.60:(k):z53_HM142067_other.z53__1497 LN:1497 @SQ SN:oafA__1830 LN:1830 @SQ SN:oafA-O-4_full__332 LN:332 @SQ SN:oafA-O-4_5-__325 LN:325 @SQ SN:sdf_I_AF370707__333 LN:333 @SQ SN:tyr-O-2__608 LN:31 @SQ SN:tyr-O-9__609 LN:32 @SQ SN:gntR-family-regulatory-protein_dt-negative__291 LN:291 @SQ SN:gntR-family-regulatory-protein_dt-positive__291 LN:291 @SQ SN:O:23-gene1__1029 LN:1029 @SQ SN:O:22-gene1__1071 LN:1071 @SQ SN:O:23-gene2__1146 LN:1146 @SQ SN:O:22-gene2__1023 LN:1023 @SQ SN:O:23-gene3__454 LN:454 @SQ SN:O:22-gene3__411 LN:411 @SQ SN:fljB_1,5_Bareilly_CFSAN000189__1511 LN:1511 @SQ SN:fljB_1,5_Idikan_SRR1272896__1511 LN:1511 @SQ SN:fliC_f,g_Salmonella.enterica_Adelaide_SRR1068324__1518 LN:1518 @SQ SN:fliC_d_Salmonella.enterica_Livingstone_SRR1299429__1521 LN:1521 @SQ SN:fliC_l,v_from-Nchanga_SRR1153349__1503 LN:1503 @SQ SN:fliC_d_from-II-48:d:z6_SRR1168371__1521 LN:1521 @SQ SN:fljB_z6_from-II-48:d:z6_SRR1168371__1503 LN:1503 @SQ SN:O-41_wzy-from-Waycross-SRR1233896__1221 LN:1221 @SQ SN:O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254__1002 LN:1002 @PG ID:bwa PN:bwa VN:0.7.17-r1188 CL:bwa mem -k 17 -t 4 H_and_O_and_specific_genes.fasta forward_25k.fastq.gz reverse_25k.fastq.gz M01659:202:000000000-BLMFJ:1:1101:20726:2390 81 O:23-gene1__1029 517 60 251M = 335 -433 TTTTCCGCAGTAAGTCTTCGTTATTTTAATCCTACTGGTGCTCATAAATCAGGTATGATTGGGGAAGATCCTAATGGAATACCAAATAACCTCATTCCATATATATCACAAGTTGCCACTGGAAAACTTAAATATTTAAATGTATATGGTGGTGATTATGACACAATTGATGGCACTGGCATGCGAGATTATATTCATGTAGATGATTTAGCTGAAGGACATGTCAAGACATTAGAATACATGTTATCAAC EGGGCFHHHHHHHHGGFGGGHHHHHHGHHFHHHHHGHHHHHGHHHHHHHHHHHHHGHHGHHHHHHHHHHHHHHHHHHHHHHGIHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGHHHHHGHHHHHHHHHHHHGHHHHHHHGHHHHGGGGHHHGIGHIHHIHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGGGGGGGGFFFFFFFCCBCA NM:i:1 MD:Z:194A56 MC:Z:251M AS:i:246 XS:i:0 M01659:202:000000000-BLMFJ:1:1101:20726:2390 161 O:23-gene1__1029 335 60 251M = 517 433 CTGCAATGCAAAGTGCAAATGTAAATAATTTGATTTTTAGTTCGTCTGCTACCGTATATGGTTGTTCTTCGATTGTTCCAAATAAAGAGAACGATACAATTGGGGGGACTACAAATCCCTATGGAACATCAAAATATTTTAGTGAGATTATTCTGCAGGATTTTTGTAAGTCTAATGAGTTATTTTCCGCAGTAAGTCTTCGTTATTTTAATCCTACTGGTGCTCATAAATCAGGTATGATTGGGGAAGAT BBBBBFFFFFFFGGGGGGGGGGHHGHHHHHGHGHHHHGGHHGHGGGHGHHHGEEFEHHHHHGFGEHHHHGFHHHGHHHGGHHHHGFGHFGHHFAHGGHFHHHHHGGGCFHHHHHGHGHHHHHHEHHHHHHHHHHHHHHHHGGHHHHFFFGGGGGGFFFG.FGFGGGFFFGGGGGFFGGFFGFGGGFF0A?B=AF/9FFFFE?BFFFFFFFFFFFFE/BFFFFFBF/FF:;BFFFFBBFF/BBFEFA..D./ NM:i:0 MD:Z:251 MC:Z:251M AS:i:251 XS:i:0 M01659:202:000000000-BLMFJ:1:1101:13382:2591 81 fliC_m,p,t,u_Salmonella.enterica_Haelsingborg_AY353410_g,m__1527 1107 0 251M fliC_g,s,t_Salmonella.enterica_Missouri_AY353405_g,m__1518 725 0 TAAAATTACAGTAAATGGGGCTGAATATACTGCTAACGCCGCGGGTGATAAGGTCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTAAGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTCAAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACC 9FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFGGAGGGGGGGGGGGGGGHFHGHGHGHHHHHGHHGGHHGHHHHHHHHHHHHHHHHHGHHGGGGGHHHHHFHHHGHHHHHHHHHGGDDGGGGGGGGGHHHHGHHHHHHGGGGGGHHFEHHHHHHGHHHHHHHHHHHHHHHGHHHHHGHHHHHHGGGGGHHHGGGGHHHHHHHHGGGGHHHHHHHGHGGFEGGHHGGGGGGGGGGFFFFFBCCCCCB NM:i:0 MD:Z:251 MC:Z:251M AS:i:251 XS:i:251 M01659:202:000000000-BLMFJ:1:1101:13382:2591 161 fliC_g,s,t_Salmonella.enterica_Missouri_AY353405_g,m__1518 725 6 251M fliC_m,p,t,u_Salmonella.enterica_Haelsingborg_AY353410_g,m__1527 1107 0 ACACTGCGGTTAACCTATTCAAGACGACTAAATCTACTGCTGGTACCGATGAAGCCAAGGCGATAGCTAGTGCCATTAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGTGTGTCTTTTACTATTGATACAAAAGCTGGTAATGACGGTAATGGTACGGTTTCTACTACTATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGCTGGTGCAGCGAATGTTAATGATGCCACCTTA AAAABFFBBBBBGGGGGGGGGGHHHGGGGGHHHHCHGHHHHHGFFHHGGFGHHF3GHGHGEGGFDGHHHHHFFGFHHHHHHGFFGEHGHHHHHGHHHHHHGHHHHHHHHHGFDGHBFGEGFHFFFFFHHGHHHHGHHHGHFHHEHHHHHEFGD@?GFHFH1?GGCGFDHHGFHHHHHHGHGGHFHHEHFD<DDDFFCGHHGHHHCGGAEF?HHEGFGF.-BFAFFEFBFGGGGFGGGE/B/;/BFFBFFFF NM:i:0 MD:Z:251 MC:Z:251M AS:i:251 XS:i:246 M01659:202:000000000-BLMFJ:1:1101:12690:3621 97 fliC_d_Muenchenstr_AOXN01000006_b,d,j__1509 1 0 215S33M fliC_g,m_Enteritidisstr_ALGF01000038_g,m__1506 1 0 ATCGGCAATCTGGAAGCAAAGTTTAATGATAATTTTGCAAAAATAATGCGTGGAATAATGATGCATAAAGCGGCTATTTCGCAGGCTAAGAAAAAGATCGGGGGAAGTGAAAAATTTTCTAAAGTTCGAAATTCAGGTGCCGATACAAGGGTTACGGTGAGAAACCGTGGGCAACAGCCCAATAACATCAAGTTGTAATTGATAAGGAAAAGATCATGGCACAAGTCATTAATACAAACAGCCTGTCG ABCABBCCFFFFGGFGGGGGGGHHHHHHCHHHHHHHHHHFHFHHHHHHHGEGGDHHHHHHHHHHHHHHHBHGGGGGHGHGFGGGGGHHHHGHHHHGGHHHGGGGGGGGHHHHGHHHHHHHHGHHHHHGHHGHHHGHGGHHHGGGGGHHGHGGHHHGCGHGHHGHHHGEECGGFGHHHEGGGGGGGGGGGGGGGGGBFGGGGGGGGGGGGGGGFFFFFFBFEFFFFBFFFFFFFFFFFFFFFFFFFFFE NM:i:0 MD:Z:33 MC:Z:119S132M AS:i:33 XS:i:33 M01659:202:000000000-BLMFJ:1:1101:12690:3621 145 fliC_g,m_Enteritidisstr_ALGF01000038_g,m__1506 1 0 119S132M fliC_d_Muenchenstr_AOXN01000006_b,d,j__1509 1 0 TTCGGGGGAAGTGAAAAATTTTCTAAAGTTCGAAATTCAGGTGCCGATACAAGGGTTACGGTGAGAAACCGTGGGCAACAGCCCAATAACATCAAGTTGTAATTGATAAGGAAAAGATCATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTCCGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGAT -;DABB/FFFFFFFFFB:.B;/B0BC.AACBFFBCBGGFAA--??GGFGGGG.HGDFHGGEHFGFEE<-@CCHD0HHHGFFGBHHHGFBGFFHHGC1<DHFHGGHHEHHHDBGGHFHFHHGGBGFDF3BFFGFGHHGGGHHHHHGGGGFGGGHGHHFFGHGHHHHHFFHGHHHHGHGEFDFFHHGBFEHHGFHHHGGGE0F5BGHGGGCGHGFGGHFAHG2DGGFGGGHGGGGGGGGGGAAFFBBAABAA> NM:i:0 MD:Z:132 MC:Z:215S33M AS:i:132 XS:i:132 M01659:202:000000000-BLMFJ:1:1101:8195:4770 97 fliC_g,t_Salmonella.enterica_Agodi_AY353407_g,m__1518 194 0 251M fliC_g,m_Enteritidisstr_ALHV01000088_g,m__1506 371 0 CCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGTGCGCTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTCCGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACGGCGTTAAGGCCCTGTCTCAGGACAACCAGATGAAAATCCAGGTT >AAA?>A11AAAEG?AAA0EEEED2DGFFBFEC?EEFFFFHG1FFB1A1EE@/B1@@1@DGHHEGHDFEGC?FGGG1GE>A/>>E?EECEFEGHBFGFFH2BFFHGHH1FCGC/CCG111<>112>GFGGC/GB1DDGFFHFDHH1<GFHHGB<<DBG0D/.-<./C<</:./GGG.:..-.9;A-9B000:0;B//:9/;B0B0FA?-99-;E///-;--9;/;BF//-9-9-:9-;BB;FB/9//9/9/ NM:i:3 MD:Z:208T5A1T34 MC:Z:250M AS:i:236 XS:i:236 XA:Z:fliC_g,s,t_Salmonella.enterica_Missouri_AY353405_g,m__1518,+194,251M,3;fliC_g,s,t_Salmonella.enterica_Senftenberg_AY353406_g,m__1518,+194,251M,4;fliC_f,g_Rissenstr_AHUI01000019_g,m__1506,+194,251M,4;fliC_g,z62_Salmonella.enterica_II.9,46:g,z62:-_AY353415_g,m__1515,+194,251M,5;fliC_g,z62_Salmonella.enterica_II.50:g,z62:e,n,x_AY353416_g,m__1515,+194,251M,5; M01659:202:000000000-BLMFJ:1:1101:8195:4770 145 fliC_g,m_Enteritidisstr_ALHV01000088_g,m__1506 371 0 250M fliC_g,t_Salmonella.enterica_Agodi_AY353407_g,m__1518 194 0 ATCGCGATTCTAATCAGACTCAAATCAACGGTGGTAAAGGCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCGTCGATCTGCAAAAAATTGATGTGAAAGGCCGTGGCCTTGATGGGTACAATGTTGAGGGGCCAAAAGAAGCGACAGTGGGTGATCTGAAATCCAGCTTCAAGACAGTTACGGGTTACGACTGCTACGCAGCGGGTGCCGATAAATATCG ;-9:-//B;//FFB9;/BA//;//:-;9--9/B090;/..;//90/BFB0FA;;00;00000;990/;./.....0C:C.:;</0DD=0=.DD00DCC>-<-./<?1111A<>222@1<@22@211@/</@>/<?/1111FFGF22B21BEF0BB/?//GF/GF@BFEF/GFBB1>/F0FGFCG@2FD1B1A0B11B12ABA1D12/A/EAA1FA0F/BB12000B0B00EE0A11?CA3333D11>111 NM:i:16 MD:Z:6T16T1T7T5T61A26A3T14T7A1T46A0T15A0C3T23 MC:Z:251M AS:i:170 XS:i:170 M01659:202:000000000-BLMFJ:1:1101:20739:5221 97 gntR-family-regulatory-protein_dt-positive__291 111 0 124M gntR-family-regulatory-protein_dt-negative__291 111 0 ATCCAACTACGATCTTGATGTAGATCCCACTCCTGCATTTTTCCTGAGAAACGATTTGACTTAGTTTTTGTATGGGAATAATTTCTCCTCGTCAGCATTGGATACAATATCATATATCATTGAT AAAAA1CBFC1A1GFFGDGFA3F3GHHHFGAGEGFGGGFGDHCHFEGHFDF0//AG/FGHBG1GBGHHEEADGGH00FGBDHHHBGHFHGG>EHEFGDE@11F2CGGFFFHDEDF2D@@FGFBE NM:i:6 MD:Z:3T3C30C49C0T4A29 MC:Z:124M AS:i:96 XS:i:96 XA:Z:gntR-family-regulatory-protein_dt-negative__291,+111,124M,6; M01659:202:000000000-BLMFJ:1:1101:20739:5221 145 gntR-family-regulatory-protein_dt-negative__291 111 0 124M gntR-family-regulatory-protein_dt-positive__291 111 0 ATCCAACTACGATCTTGATGTAGATCCCACTCCTGCATTTTTCCTGAGAAACGATTTGACTTAGTTTTTGTATGGGAATAATTTCTCCTCGTCAGCATTGGATACAATATCATATATCATTGAT 11BHFFFHCF@1FFGFHFDBFGF@//EGF/GF1F1FHG>G0BFHFHGGCEG?HHGDBBD11HGE/FHGHFFHGGA2G21DHGG0A0?E0GFHFAFA3AA33GGA33F3AEFGFFFFDDB111A> NM:i:6 MD:Z:3T3C30C49C0T4A29 MC:Z:124M AS:i:96 XS:i:96 XA:Z:gntR-family-regulatory-protein_dt-positive__291,-111,124M,6; M01659:202:000000000-BLMFJ:1:1101:11251:5664 81 fliC_f,g,t_Salmonella.enterica_Berta_AY353532_g,m__1527 1421 0 107M41S fliC_f,g,s_Salmonella.enterica_Agona_AY353384_g,m__1518 1412 0 CGGAAGTTTCTAATATGTCTAAAGCGCAGATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAATCCGGCGATTGATTCACCGACACGTGGTACACAATCAAGGC DHHHFCFD1D1HFHHGHHFFEGGGGHHHHHHGCHHHHFHHGHGHHHHHGGFGGHFG@FGGGHHFGGGHHGFHFFEEEGGHGGGEEGGHGFHGBBHHGEGFFEGFHGGGGFFDEDHHHHHHGECGGHGGFFGGGGGFFDFFFFFBBBBB NM:i:0 MD:Z:107 MC:Z:107M41S AS:i:107 XS:i:107 M01659:202:000000000-BLMFJ:1:1101:11251:5664 161 fliC_f,g,s_Salmonella.enterica_Agona_AY353384_g,m__1518 1412 0 107M41S fliC_f,g,t_Salmonella.enterica_Berta_AY353532_g,m__1527 1421 0 CGGAAGTTTCTAATATGTCTAAAGCGCAGATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAATCCGGCGATTGATTCACCGACACGTGGTACACAATCAAGGC 3AA?AACFFFFFGGGGGGGGGGHGHGGGGGHHCHHHHHHGHHGHHGBGFHFHGFHHFFFHHCDFC0EAEEEGHHGHHHHDFGGGHHG1GAEGFHHHHGHHHHGGGGEDHFGDFG?CCFFGHH1GHDGG?FG0..<DGBGHGHF0<GFE NM:i:0 MD:Z:107 MC:Z:107M41S AS:i:107 XS:i:107 M01659:202:000000000-BLMFJ:1:1101:15808:5869 137 fliC_f,g,s_Salmonella.enterica_Agona_AY353384_g,m__1518 1417 0 102M149S = 1417 0 GTTTCTAATATGTCTAAAGCGCAGATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAATCCGGCGATTGATTCACCGACACGTGGTACACAATCAAGGCAGCGAAAGCTGCCTTTTTTAATTCCGGAGCCTGTGTAATGAAAGAAATCACCGTCACTGAACCTGCCTTTGTCACCCGCTTTTCCTGTTCTGGCTCGGCCTGTCGCGA A>AABFFFFFFFGGGGGGGGGGGGGHHHHHHHHHHHHGHHGHHGHHHGGHGGFHEH?EFE?EGGGGGHHGHHHHGGGGFHHGFFGGHHHHFHHHHHHGGDGGFHHGGGGGGHGFGFFFHGDDGFGGFHGHGFGGHFHHHHHFEHGGGGCGGCHHGFHHHHFGGGGFGF/BA?9EFFCFFFGGGEBBFF?FF/BFBD9A.DFFEFF?FFFFF9FF/:BBB.B--9AFBFFEBFFFFFFFFFFFA..:F?A;; NM:i:0 MD:Z:102 AS:i:102 XS:i:102 M01659:202:000000000-BLMFJ:1:1101:23876:5926 81 fliC_g,s,t_Senftenbergstr_AOXW01000066_g,m__1506 402 0 250M fliC_g,m_Enteritidisstr_ALHN01000008_g,m__1506 299 0 TGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTGCAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAAATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCAGGTGCTGTAGTAACT B/BFFFFFFFFB:0BFFFBGDDFFEGFFF0FGGFB/FFF?GFFGEHGGHHHFGC00HHFHG<EHHG0<DGHFHFHGGFFCGHHHHHDHHHGFHHHHHFHFHHHHHF2@DBGCAGHGHHHHEGBGHHFGFHGFHHHHGHGHEHHFGGGHHHHHHHGHGFFGFBGFHGF4HHHHHHHGFGEGHHEGEA?GFFFFHHHHFGGFEDGFCECFGFFFHFFHCEHFBHGFFCHCGGGGGGFGGGFFFFFFFBCCCB NM:i:0 MD:Z:250 MC:Z:251M AS:i:250 XS:i:250 M01659:202:000000000-BLMFJ:1:1101:23876:5926 161 fliC_g,m_Enteritidisstr_ALHN01000008_g,m__1506 299 0 251M fliC_g,s,t_Senftenbergstr_AOXW01000066_g,m__1506 402 0 CTAACGGGACTAACTCTGATTCCGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACGGTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTGCAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTG AA3AAABB2DFFGGGGGGGGGGHGFGGFFFFFGHHFFDCGHBFHHGHHEFHEFFHHFGHHFEF5EGGHHHHGHGHGGGEGGHHHHHHHGHHFHHHGHHHHGGGEHEEFGHHFFGHHGHGHHHHHAFHHGGFHHGDGHHH1FFFB1FGDEFFGF>GGGHGGFGFGHHHGHFDHBDGHF0.GGHHGGHEC@CFG0CGFGGFHHHHAGHFB/:C/C9;00.B?FGBFFBFB0FF0:...9B./A.B9@?>--:9 NM:i:0 MD:Z:251 MC:Z:250M AS:i:251 XS:i:251 M01659:202:000000000-BLMFJ:1:1101:8912:6914 81 O:23-gene2__1146 312 60 185M = 312 -185 GGGATCGCTTGCCGCATATTATGCTGGTGTTCATAAGATTATCGCGATGCTTGAAGGGTTAGGTTTTTTATTTACCGAACAACCATCTGGGATTCCCCAAAAGACAAAAATCCTAAAAAGAATACAGATTCTGCTCTATAGAATAGCTTTTAAGAAAATTAATACACTTATTGTACTTAATGAAG HGGHGGHGGGGGGGHHHHHHHGHGHGHHHHHHHHHHBHGGGGGGGHHHHHHHHHHHHHHHHGGGGHHGHHHGHGGGHHGGHHHHHHHHHHHHGGGGGHHHHHHHGHHHHHHHHHHIIIHHHHHHIHIHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGFGFGGGGFFFFFFFFCCBAA NM:i:0 MD:Z:185 MC:Z:185M AS:i:185 XS:i:116 M01659:202:000000000-BLMFJ:1:1101:8912:6914 161 O:23-gene2__1146 312 60 185M = 312 185 GGGATCGCTTGCCGCATATTATGCTGGTGTTCATAAGATTATCGCGATGCTTGAAGGGTTAGGTTTTTTATTTACCGAACAACCATCTGGGATTCCCCAAAAGACAAAAATCCTAAAAAGAATACAGATTCTGCTCTATAGAATAGCTTTTAAGAAAATTAATACACTTATTGTACTTAATGAAG A?>AABBBFB@AGCCCEGGGFGHHHHHGFGFGBHFF5BFGHGHHGGAEEGHHHGEFGFFHHFEEFHGGGEHHHHHHGGGGGHHGGGGFHHHHHHHHHHHGHEHGHGHHHHGHFHHHHFHGGHHHHHHHHHGGHGFHHFHHHHHHGHGBDGHHGHHBFHHHFEHHGFHHBGHHHHHHHHFHHFHDG NM:i:0 MD:Z:185 MC:Z:185M AS:i:185 XS:i:116 M01659:202:000000000-BLMFJ:1:1101:27485:7939 81 fliC_g,s,t_Salmonella.enterica_Missouri_AY353405_g,m__1518 1122 0 251M fliC_g,s,t_Salmonella.enterica_Senftenberg_AY353406_g,m__1518 813 0 ATATACTGCTAACGCCGCGGGTGATAAGGTCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTAAGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTCCCGCTAGCCCACTGGCTTCAATTGATTCTGCATTGTCAAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGGTAACCAATCTGA F////BFBEB@@@@@@@@-FFFBFFFFFFC9099C0GEBC909.;0;/BC0F0B;0BFFB;/FF;::///.C??A.GGC0DD0GFG<0D0GHHDDCCE>-<--@A/F/1?@DF>>1D1FC>//B1B0B/FBFF0GAG1GF1EBHHHFBFFBFGE1EGF1HHFD1>/EGGHHF>/E/0HEB10FGAEGFF1AF22A/0CAAAEA0ADGFDF1FGBHF2BFA0EAFAFGCBF3ABGGA11GD111DFFAAAAA NM:i:2 MD:Z:121A6A122 MC:Z:248M AS:i:241 XS:i:241 M01659:202:000000000-BLMFJ:1:1101:27485:7939 161 fliC_g,s,t_Salmonella.enterica_Senftenberg_AY353406_g,m__1518 813 0 248M fliC_g,s,t_Salmonella.enterica_Missouri_AY353405_g,m__1518 1122 0 GGAAGGAGATACCTTTGATTATAAAGGAGTGTCTTTTACTATTGATACAAAATCTGGTAATGACGGTAATGGTACGGTTTCTACTACTATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGCTGGTGCAGCGAATGTTAATGATGCCACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTGACTTTTGATGATAAAACTAACAAAGAGAGTGCGAAACTTT 1A1A1ACA1C11AGBGG3GFGG3AF110AFC33EDDF3B1FGFH22211BFE1BDFBG12DEDEAE?CBAAB12DECF/EHHGFHFB1EG1GFEFFB@GDFHA/1BF2/0BF/F2D@1>CEGGGE2FGHEECG@>0FDGDBE/CGFB2FFFHBGHBF11<011111111<11F010<FG11F11111111==FG>FFHFG...<C==0D0D=D0F:;C000;C00000/:0.::CFA/;;AC-9@FE0 NM:i:6 MD:Z:27T24G154T17C2A2C16 MC:Z:251M AS:i:218 XS:i:218 M01659:202:000000000-BLMFJ:1:1101:24516:8087 73 fliC_m,t_Salmonella.enterica_Oranienburg_AY353412_g,m__1527 1474 0 54M197S = 1474 0 GTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAATCCGGCGATTGATTCACCGACACGTGGTACACAATCAAGGCAGCGAAAGCTGCCTTTTTTAATTCCGGAGCCTGTGTAATGAAAGAAATCACCGTCACTGAACCTGCCTTTGTCACCCGCTTTTCCTGTTCTGGCTCGGCCTGTCGCGACCACTGTTGTAAGGGCTGGAAAATCACGCTGGATAAGACGACGGTCAA CCCCCFFFCCCCGGGGGGGGGGHHHHGGGGGHHGHHGGHHHHHHHHHHHGGGGGHHHGGGGGGHGHHHHHHHGGGGGGGHGHHHHHHGHHHHHHHHGGGGGGGGHHHHHHHHHGHHHHHHGDGGGGHHHHHHHHHHHHHHGHHHHHHGHGGGHHHBGHHGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFFFFFEFFFFFCFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFADDF NM:i:0 MD:Z:54 AS:i:54 XS:i:54 M01659:202:000000000-BLMFJ:1:1101:16523:9396 81 fliC_g,m,s_Montevideostr_AHIK01000035_g,m__1506 1 0 161S90M fliC_g,m_Enteritidisstr_ALGC01000031_g,m__1506 1 0 ATAATGATGCATAAAGCGGCTATTTCGCAGGCTAAGAAAAAGATCGGGGGAAGTGAAAAATTTTCTAAAGTTCGAAATTCAGGTGCCGATACAAGGGTTACGGTGAGAAACCGTGGGCAACAGCCCAATAACATCAAGTTGTAATTGATAAGGAAAAGATCATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTCCGCTATTGAG FFFFFFFFFFFFFFFFDGGGGGGGAGGGGGGGGGGGGGGGGGGGGGHHHHHHHHHHHHHHHHHHHHHHHHHGHGHHHHHHHGGGF@GHGHHHHHHHGGHFGHHHHHHGGFGGGHHHHHHHGHHHHHGHHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHHGGGFGCGHHHHHHHGHHHHHHHHHHGHHHHHHHHHHHHHGHHGGGGGGGGGGGBBBFFFFBBBBA NM:i:0 MD:Z:90 MC:Z:195S56M AS:i:90 XS:i:90 M01659:202:000000000-BLMFJ:1:1101:16523:9396 161 fliC_g,m_Enteritidisstr_ALGC01000031_g,m__1506 1 0 195S56M fliC_g,m,s_Montevideostr_AHIK01000035_g,m__1506 1 0 GTTTAATGATAATTTTGCAAAAATAATGCGTGGAATAATGATGCATAAAGCGGCTATTTCGCAGGCTAAGAAAAAGATCGGGGGAAGTGAAAAATTTTCTAAAGTTCGAAATTCAGGTGCCGATACAAGGGTTACGGTGAGAAACCGTGGGCAACAGCCCAATAACATCAAGTTGTAATTGATAAGGAAAAGATCATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAA AAAA?FFDFFFFFFGFGGGGFFHGHHHHHGGGGGGHGHHHCFGFEHHHFHHEC?FEHHFHHGGDCDFHHHHHFFFEGHFA1EECE/?GGHGEFGGHFGFHFEGFHHHGEHFHHEGGH3B2FDB@DCDHGHGGFHHFGHFFFFFHHHCEHGGAGFFHHGHGEHHBGFHGBGFGCFHHFGFHHGFFGGGGGBBFAFFGGGGGGGGGGG0CFGGFFGBFF0;AB.ABFFFEEFD9//9BFFFFE/;FB/;FFFB NM:i:0 MD:Z:56 MC:Z:161S90M AS:i:56 XS:i:56 M01659:202:000000000-BLMFJ:1:1101:13999:9488 81 O:23-gene1__1029 311 60 76M = 311 -76 TCACAGGTACCTTGACTCTACTGGCTGCAATGCAAAGTGCAAATGTAAATAATTTGATTTTTAGTTCGTCTGCTAC HHHHHHHHGHHGHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHGGGGGGGGGGCDCFFFFCCCCC NM:i:0 MD:Z:76 MC:Z:76M AS:i:76 XS:i:0 M01659:202:000000000-BLMFJ:1:1101:13999:9488 161 O:23-gene1__1029 311 60 76M = 311 76 TCACAGGTACCTTGACTCTACTGGCTGCAATGCAAAGTGCAAATGTAAATAATTTGATTTTTAGTTCGTCTGCTAC CCCCCFCFFFFFGGGGGGGGGGHHHHGGHHHHHHHHHGHHHGGHHDGHHHHFHHHHHHHHHHHHFHIGGGGGHHHH NM:i:0 MD:Z:76 MC:Z:76M AS:i:76 XS:i:0 M01659:202:000000000-BLMFJ:1:1101:20513:9766 97 O:23-gene1__1029 867 60 119M = 867 119 CTATAATATTGTCGCGCGAAGAAATGGTGATTTAGACAAATCTTGGGCTGATACTGAAAAAGCCAGAAACCTCCTGGGGTGGGAGGCAAAATATGGAATAGAGGATATGTTGCAAGATG BBBBAFF@DDFFGEGG?EAAF?FEA535A5BABABGDA2GH355AFFAGD1AFGHD5GHHH1GEHHGB3?1BGFFE3EEFE/EAFGGE0BE3GHH3333BD3B0GCDGF4F44F???DD NM:i:1 MD:Z:15A103 MC:Z:119M AS:i:114 XS:i:0 M01659:202:000000000-BLMFJ:1:1101:20513:9766 145 O:23-gene1__1029 867 60 119M = 867 -119 CTATAATATTGTCGCGCGAAGAAATGGTGATTTAGACAAATCTTGGGCTGATACTGAAAAAGCCAGAAACCTCCTGGGGTGGGAGGCAAAATATGGAATAGAGGATATGTTGCAAGATG D2FFHHHHEEE//E///2@EGF1FDFCHHEEGDFF@DHFE0FGFAA122AAAHFGHGGCGBB1BGDGFFCEHGCGCFEFFGEHFGFAFGDGBFGGDBGFGEBEBGBFFFF1FFFAAA1A NM:i:1 MD:Z:15A103 MC:Z:119M AS:i:114 XS:i:0 M01659:202:000000000-BLMFJ:1:1101:9746:9829 73 fliC_z4,z23_Salmonella.enterica_I.8,20:z4,z23:-_AY353544_z4,z23__1269 1211 0 59M192S = 1211 0 CTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAATCCGGCGATTGATTCACCGACACGTGGTACACAATCAAGGCAGCGAAAGCTGCCTTTTTTAATTCCGGAGCCTGTGTAATGAAAGAAATCACCGTCACTGAACCTGCCTTTGTCACCCGCTTTTCCTGTTCTGGCTCGGCCTGTCGCGACCACTGTTGTAAGGGCTGGAAAATCACGCTGGATAAGACGACG CCDDCCFFFCFFGGGGGGGGGGGGHHGHHHHGGGGGHHGBGGGHGHHGHHHHHHGGGGGHHHGGGGGGHGHHHHHHHGGGGGGHHGFHHHHHGHHHGFFGHDGGGGGGHHHHHHHHHHGGHHHHHHGGGGGHHHHHHHHHHHHHGHHHHHHHGHGGGBHGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFDFFFFFFFFFFFFFFA NM:i:0 MD:Z:59 AS:i:59 XS:i:59 M01659:202:000000000-BLMFJ:1:1101:22387:10758 185 fliC_g,s,t_Salmonella.enterica_Senftenberg_AY353406_g,m__1518 80 0 218M = 80 0 CCGCTATTGAGCGTCTGACCTCTGGTCTGCGTATCAACAGCGCGACAGACGATGCGGCAGGCCAGGCGATAGCTAACCGCTTAACTTCTAATATCAAAGGTGTGACTCAGGCTTCCCGCAACGCTAACGCCTGCATGTCTATTGCGCAGACCAGTGAAGGTGTGCTGAATGAAATTAACAGCAACCTGCAGAGTGTGCGTGAGTTGTCTGTTCAGGCC >9/9/F:9BA@@C;;///..:./9A99.A.;0F009.@:A-C:C:.C.<.-CCC->0>1<0CC<</??1111?/////@12>111>1222GGF2>B10<11111B00010///<//>?//?/1//>/>B011B11@1D1BBEAA/BB211A12111B0EB0B112FA222222F22B1A10FAB01F1AAA0E00EB1A111AB111CDBBB11111> NM:i:13 MD:Z:17T27A24T11C18C16T10A1G4T16C8C17A10C26 AS:i:153 XS:i:153 M01659:202:000000000-BLMFJ:1:1101:22383:10770 97 fliC_g,t_Salmonella.enterica_Agodi_AY353407_g,m__1518 80 0 218M fliC_g,s,t_Salmonella.enterica_Senftenberg_AY353406_g,m__1518 80 0 CCGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCTTCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGTGCGCTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCC CCDDCCCFFFFFGGGGGGGGGGHGHHHHHHGGGGHHHHHHHGGGGGGGHHGGGGGGGGGGGGGHHHHGGGHGHHHHHHGFGGGHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHGHGGGGGGGGHGGGGGGGGHHHHHHHHHGGGGGHHHHHGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFFFFFFFFFFFFFFFFDFFFFFFFFFFFFFFFF NM:i:0 MD:Z:218 MC:Z:218M AS:i:218 XS:i:218 M01659:202:000000000-BLMFJ:1:1101:22383:10770 145 fliC_g,s,t_Salmonella.enterica_Senftenberg_AY353406_g,m__1518 80 0 218M fliC_g,t_Salmonella.enterica_Agodi_AY353407_g,m__1518 80 0 CCGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCTTCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGTGCGCTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCC FFFFFFFFFFFCEFAFA.GEGFFEGGGGGEGGGFGFGGGGFGCGHGHHHGGGGCGFHGHHHAHGGGGHHHHHHGGGGGHHHHHHHHHHHHHHHHHHHFHHHHHHGHHHGHHGGGGGGGGGGGHGHGGGGGGHHHHGGBHHGGGGGHHHGHHHHHHHHHGGGGGHHHHHHHHHHHHGHHHHGHHHHHHGGGGGHGGGGGGGGGGGGGFFFFFFCCCBAA NM:i:0 MD:Z:218 MC:Z:218M AS:i:218 XS:i:218 M01659:202:000000000-BLMFJ:1:1101:19007:10881 97 fliC_f,g,t_Salmonella.enterica_Berta_AY353532_g,m__1527 1411 0 117M134S fliC_f,g,s_Salmonella.enterica_Agona_AY353383_g,m__1518 1429 0 GACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAGATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAATCCGGCGATTGATTCACCGACACGTGGTACACAATCAAGGCAGCGAAAGCTGCCTTTTTTAATTCCGGAGCCTGTGTAATGAAAGAAATCACCGTCACTGAACCTGCCTTTGTCACCCGCTTTTCCTGTTCTGG ACCCCFFFFFFCGCGGGGGGGGHHHHHHHHHHHHHGGCGGHHHHHHHHHHHHGGGFGHHHHFGGHHHGHHHGGGGGGGGGGGHGGHHHHGGGGFHGGHHGGHHGHHHHHHHHGGGGGHHHGGGGGCHGHHHHHHFGGGGGG<GFGHHHHHGHHGHGHHGGGGGGGGGGGGGGGGGGGGGGGGFGGGGFFFFFFFFFFFFFFFFFFFFFFFFFDFFFFFFFFFFFFFFFFFFFFFFAFFDEFFFFFFFFFFF NM:i:0 MD:Z:117 MC:Z:90M161S AS:i:117 XS:i:117 M01659:202:000000000-BLMFJ:1:1101:19007:10881 145 fliC_f,g,s_Salmonella.enterica_Agona_AY353383_g,m__1518 1429 0 90M161S fliC_f,g,t_Salmonella.enterica_Berta_AY353532_g,m__1527 1411 0 TCTAAAGCGCAGATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAATCCGGCGATTGATTCACCGACACGTGGTACACAATCAAGGCAGCGAAAGCTGCCTTTTTTAATTCCGGAGCCTGTGTAATGAAAGAAATCACCGTCACTGAACCTGCCTTTGTCACCCGCTTTTCCTGTTCTGGCTCGGCCTGTCGCGACCACTGTTGTAA FB999-DFF/B/BFFFFFFEFFFE?FB/://?EFDD9FAB;.ACA.A:-@F9/FF.EDB--@/9.FEDGGEGFEGFB;;0A?AAFFF0DE;GDACFHGHHGHHFGCGDFHHHGHHGBHFGGFHBHHHHFDCDE/DHGEGGGHGGGFHHHGHGGGGGGHFGHHGHHGHFFHFHHGHHEFC?1GGHFGEHHGGFGGHHFHHHHGG>>CGGHHHGFHHHHGHHHHGGGGGGGGCGGGGCGGGFFFC4FFAAABA NM:i:0 MD:Z:90 MC:Z:117M134S AS:i:90 XS:i:90 M01659:202:000000000-BLMFJ:1:1101:28780:10887 97 fliC_g,s,t_Salmonella.enterica_Senftenberg_AY353406_g,m__1518 109 0 249M fliC_g,m,s_Montevideostr_AETU01000047_g,m__1506 288 0 CGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCTTCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGTGCGCTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTCCGATCTGAAATCTATCCAGGATGAAATTCAGCAACGT AA>AACFFFFFFGGGGGGGGGGGGGGGGCFGGEFEFAGFGGHGHGHHHGG@EFEFHHHFHHHHHHHHHHFHFFHHHHHHHHGHHHGGHG?EGGGGGGGHGGGFGGGGHGHHFHHHHGGGGGHHFHHHFHHGGFHDCGFDFHHHHHHFHHHHHGHHGGGGGGGGGFDGGGGGGGGFGGGGGFFGGFFFFFFFFFFFFFFDFFFFFFFFFFFEFFFD?DFFF/BFFFFFE/BFBEBFFEFFFFFFFFFFFE NM:i:0 MD:Z:249 MC:Z:251M AS:i:249 XS:i:249 M01659:202:000000000-BLMFJ:1:1101:28780:10887 145 fliC_g,m,s_Montevideostr_AETU01000047_g,m__1506 288 0 251M fliC_g,s,t_Salmonella.enterica_Senftenberg_AY353406_g,m__1518 109 0 TGTTCAGGCCACTAACGGGACTAACTCTGATGCCGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACGGTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTGCAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAG ;//BA9...00.A:9-90F9B0FFC:90/;9-9AGG00GHGHC<:0FGHF:0FGEHHFGFDHGDGC.<.0G<1BGDFEFHE>.-//@ECF>2GHFHHGDFGD2HGD3?DCHCFHFHHHFGC?0GHFGEGDGGHGFGFFFHFHHHFHGBHFFHHFAGGHGGFFHHHGEHHHHG5GFHFFFHGDEGADFBHFHGG?EHFGF5E335EFDFGACFCFA2GAEHHHHHFGGHGFFFFGFGGGGFABFFBFBBAA> NM:i:1 MD:Z:31T219 MC:Z:249M AS:i:246 XS:i:246 M01659:202:000000000-BLMFJ:1:1101:20761:10965 81 O:23-gene1__1029 675 60 219M = 675 -219 TGACACAATTGATGGCACTGGCATGCGAGATTATATTCATGTAGATGATTTAGCTGAAGGACATGTCAAGACATTAGAATACATGTTATCAACAAAAGTAGGTTATGATGTTTTTAATTTGGGGTCAGGTCGAGCATATAGTGTTTTGCAAATCATTAAAGCTTTTGAGCGCGTCACTAAAAAAGAGATTCCCTATAATATTGTCGCGCGAAGAAATGG GGGGGGGHHHHHHHHHHHHHHGGGGHGHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHGGGHHHHHGGGGGHHGHHHHHHHHHHHHFHHHHHHHHFGHHHHHHHHGGGFGGGHHGFHHGHHHHHHHHHGCHHHHHHHGGGGGGGGGFAAFFFFFBBBBA NM:i:3 MD:Z:36A133T36A11 MC:Z:219M AS:i:204 XS:i:0 M01659:202:000000000-BLMFJ:1:1101:20761:10965 161 O:23-gene1__1029 675 60 219M = 675 219 TGACACAATTGATGGCACTGGCATGCGAGATTATATTCATGTAGATGATTTAGCTGAAGGACATGTCAAGACATTAGAATACATGTTATCAACAAAAGTAGGTTATGATGTTTTTAATTTGGGGTCAGGTCGAGCATATAGTGTTTTGCAAATCATTAAAGCTTTTGAGCGCGTCACTAAAAAAGAGATTCCCTATAATATTGTCGCGCGAAGAAATGG AA??A1C1BFD1FGGCGFCFFEGHHHE0A0AFHHFHHHBFE2DEBBG1D2F1D1AGH1AEAA0AC2G2FGAEGHFHA1AFFFFHGHHHHEFGFFGFHGGHEHFHHHHFHHFFHGFHFGFGBBEEEEFGBFHGEGGGHHFGHHGFHHFAGFGBFFFGFHFGB11DGFHGGHGC<AC<CHHHGHHCFGCGDDDBGGFHHHHGHFHGH?C-@C?@A?9/0;B NM:i:3 MD:Z:36A133T36A11 MC:Z:219M AS:i:204 XS:i:0 M01659:202:000000000-BLMFJ:1:1101:21158:11838 97 gntR-family-regulatory-protein_dt-positive__291 1 0 114S136M gntR-family-regulatory-protein_dt-negative__291 1 0 GAGTATGCCGTGATTTCCATTCAGGAACATAAAAGTATTCTGCAAGCTCTTGAACTTCATGATGAAAAATTGGCACGCCAGCGCATGCGCGAACACATTATTCGCTCGATGGAGAATATGCTGACCCGCTATGTTGGTGACCCTTCTGCCTGATCTTTTCGCCTGCGTGAGCATCGCAGGCGCTTCAACCAATTCTTCAATTCTATTAATCACGTCCAGTAACGATCCAACTACGATCTTGATGTAGATC BBABBFFFFBBDGGFGGGGGGGHGHHHHHHHHFHGEGGHHHHHHHHHHHHHGGFHHHFHHHHHHHGHHHGHHFFGHGGGGFFGGGGGGGGGGGGGHHHGGHGHHGGHGGHHGHHHFGHHFHHHHHHHGGGCGHHHFHAFHFDFHHHGFBGHHBGHHHHHHGCDDHFFGGDGFHHHGGGCCDGGGGGGGGGGGFFGGGFGGGGGGGGGGGGGGGGGFGGGFFFFFFFFFBFFEFFFFFFFFFEFFFFFBFF NM:i:2 MD:Z:113T3C18 MC:Z:31S220M AS:i:126 XS:i:126 XA:Z:gntR-family-regulatory-protein_dt-negative__291,+1,114S136M,2; M01659:202:000000000-BLMFJ:1:1101:21158:11838 145 gntR-family-regulatory-protein_dt-negative__291 1 0 31S220M gntR-family-regulatory-protein_dt-positive__291 1 0 CATGCGCGAACACATTATTCGCTCGATGGAGAATATGCTGACCCGCTATGTTGGTGACCCTTCTGCCTGATCTTTTCGCCTGCGTGAGCATCGCAGGCGCTTCAACCAATTCTTCAATTCTATTAATCACGTCCAGTAACGATCCAACTACGATCTTGATGTAGATCCCACTCCTGCATTTTTCCTGAGAAACGATTTGACTTAGTTTTTGTATGGGAATAATTTCTCCTCGTCAGCATTGGATACAATAT DDD;>-A9/;9;FB:AD=;@DFFFFFB//BFBF;0B0F?AGDADBBFFA?EGBGG/CA./GE;.CBGC00C/---GC?C<@CF1FFG?GG@C0G</@CC3GHGHHHFGDG3B3FHHGDBHGGBDF?/E/?HFEGD?CEFE3HFFHHGFHHHHHFGGD4FHHHGCGEEAGFCEG55BFGAHGEHHEB5HGGHHGHHHHHHGGFFGEAGEHHHFGGAFFHHGHHGHGGEFEAGGFGGGGGCFFFFFFFBBAAA NM:i:6 MD:Z:113T3C30C49C0T4A15 MC:Z:114S136M AS:i:190 XS:i:190 XA:Z:gntR-family-regulatory-protein_dt-positive__291,-1,31S220M,6; M01659:202:000000000-BLMFJ:1:1101:22842:11880 97 fliC_g,m_Enteritidisstr_ALHO01000019_g,m__1506 1 0 206S45M fliC_g,s,t_Salmonella.enterica_Senftenberg_AY353406_g,m__1518 172 0 CTGGAAGCAAAGTTTAATGATAATTTTGCAAAAATAATGCGTGGAATAATGATGCATAAAGCGGCTATTTCGCAGGCTAAGAAAAAGATCGGGGGAAGTGAAAAATTTTCTAAAGTTCGAAATTCAGGTGCCGATACAAGGGTTACGGTGAGAAACCGTGGGCAACAGCCCAATAACATCAAGTTGTAATTGATAAGGAAAAGATCATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAG AABCCFFDFFFFGGGGGGGGGGHHHHHHHHHHHHHHHHHHGEGGGHHHHHHHHHHHHHHHHHGGGGGHHHHHGGGGGHHHHHHHHHGGHHHGGGGGGGHHHHHHHHHHHHHHHHHHHHGHHGHHHHHHGGFHFGGGGHHHHGCGHHGGFHGHHHGHHCEHGGGGGHHHGHGHHHHHHHHGGGGFGGGEGGGGGGGGGGGGGGGGGGGGGFGGGGGGFFFFFFFFFFFFFFFFFFFFFFFEFFDFFFFEFF? NM:i:0 MD:Z:45 MC:Z:5S246M AS:i:45 XS:i:45 M01659:202:000000000-BLMFJ:1:1101:22842:11880 145 fliC_g,s,t_Salmonella.enterica_Senftenberg_AY353406_g,m__1518 172 0 5S246M fliC_g,m_Enteritidisstr_ALHO01000019_g,m__1506 1 0 TTAAAATCAAAGGTCTGCCTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGTGCGCTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTCCGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACGGTGTTAAAGTCCTGTCT 9;/;//B9/FFFEFBA--B9A9--A-A;-FEE:;-C.EBA?AC-B90;;00F;;-ACGHHGC0BHGGFFHC?CCCE1HFHGFGFGDF<1EGFF?FHGHFHGGGGCHCB/GGHHGHHFHFCEHGF0EGCEHGHGGHG@F2GGD2DEG1FBHFEGEEFF2GF@GF@BB@B00BF1FHHHFHHG1FD/HFEGEEDFDG12FAFF////E/00F1DGFBFGEA1BD11GAD300EAEA13GFAD1FA1A>1A>1A NM:i:1 MD:Z:12A233 MC:Z:206S45M AS:i:241 XS:i:241 XA:Z:fliC_g,s,t_Salmonella.enterica_Missouri_AY353405_g,m__1518,-172,5S246M,1;fliC_g,t_Salmonella.enterica_Agodi_AY353407_g,m__1518,-172,5S246M,1;fliC_f,g_Rissenstr_AHUI01000019_g,m__1506,-172,5S246M,2;fliC_g,z62_Salmonella.enterica_II.50:g,z62:e,n,x_AY353416_g,m__1515,-172,5S246M,5;fliC_g,z62_Salmonella.enterica_II.9,46:g,z62:-_AY353415_g,m__1515,-172,5S246M,5;