Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: NTFQ01010417.1 Kokia drynarioides strain JFW-HI SEQ_125303, whole genome shotgun sequence Parameters: 2 7 7 80 10 50 1000 Pmatch=0.80,Pindel=0.10 tuple sizes 0,4,5,7 tuple distances 0, 29, 159, 1000 Length: 72434 ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34 Warning! 27 characters in sequence are not A, C, G, or T Found at i:382 original size:3 final size:3 Alignment explanation
Indices: 376--459 Score: 62 Period size: 3 Copynumber: 28.0 Consensus size: 3 366 TTATTAATGT * * * * * * * 376 TTA TTA TTA TTA TTG CTG TCA TTA ATA TTA TTAA TGA -TA TTA GTA 1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA * ** 421 ATA TTA TTA TTA TTA TTA TTA TTA CCA TTA TTA TTA TTA 1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA 460 AAGCCTTATT Statistics Matches: 62, Mismatches: 17, Indels: 4 0.75 0.20 0.05 Matches are distributed among these distances: 2 1 0.02 3 59 0.95 4 2 0.03 ACGTcount: A:0.35, C:0.05, G:0.05, T:0.56 Consensus pattern (3 bp): TTA Found at i:1155 original size:6 final size:6 Alignment explanation
Indices: 1144--1227 Score: 97 Period size: 6 Copynumber: 14.7 Consensus size: 6 1134 ATTTTGAAAA 1144 TAAATT TAAATT TAAA-T TAAATT TAAATT TAAGA-T T-AATT TAAATT 1 TAAATT TAAATT TAAATT TAAATT TAAATT TAA-ATT TAAATT TAAATT * * * 1190 TAAATT TAAA-A TAAATC TAAATT TAAA-A TAAATT TAAA 1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAA 1228 AGGGGTCCGA Statistics Matches: 67, Mismatches: 5, Indels: 12 0.80 0.06 0.14 Matches are distributed among these distances: 4 1 0.01 5 16 0.24 6 49 0.73 7 1 0.01 ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43 Consensus pattern (6 bp): TAAATT Found at i:1166 original size:17 final size:17 Alignment explanation
Indices: 1129--1227 Score: 96 Period size: 17 Copynumber: 5.7 Consensus size: 17 1119 CAATAATTCT * 1129 TTTAAATTTTGAAAATAAA 1 TTTAAA-TTT-AAATTAAA 1148 TTTAAATTTAAATTAAA 1 TTTAAATTTAAATTAAA 1165 TTTAAATTTAAGATT-AA 1 TTTAAATTTAA-ATTAAA 1182 TTTAAATTTAAATTTAAA 1 TTTAAATTTAAA-TTAAA * * 1200 -ATAAATCTAAATTTAAA 1 TTTAAATTTAAA-TTAAA * 1217 -ATAAATTTAAA 1 TTTAAATTTAAA 1228 AGGGGTCCGA Statistics Matches: 73, Mismatches: 4, Indels: 8 0.86 0.05 0.09 Matches are distributed among these distances: 16 1 0.01 17 58 0.79 18 8 0.11 19 6 0.08 ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43 Consensus pattern (17 bp): TTTAAATTTAAATTAAA Found at i:1170 original size:23 final size:22 Alignment explanation
Indices: 1145--1216 Score: 99 Period size: 23 Copynumber: 3.1 Consensus size: 22 1135 TTTTGAAAAT 1145 AAATTTAAATTTAAATTAAATTT 1 AAATTTAAA-TTAAATTAAATTT * 1168 AAATTTAAGATTAATTTAAATTT 1 AAATTTAA-ATTAAATTAAATTT * 1191 AAATTTAAAATAAATCTAAATTT 1 AAATTTAAATTAAAT-TAAATTT 1214 AAA 1 AAA 1217 ATAAATTTAA Statistics Matches: 44, Mismatches: 3, Indels: 4 0.86 0.06 0.08 Matches are distributed among these distances: 22 5 0.11 23 38 0.86 24 1 0.02 ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43 Consensus pattern (22 bp): AAATTTAAATTAAATTAAATTT Found at i:1835 original size:8 final size:8 Alignment explanation
Indices: 1817--1849 Score: 57 Period size: 8 Copynumber: 4.0 Consensus size: 8 1807 AAATTTTTTA 1817 TTTAAATAT 1 TTTAAA-AT 1826 TTTAAAAT 1 TTTAAAAT 1834 TTTAAAAT 1 TTTAAAAT 1842 TTTAAAAT 1 TTTAAAAT 1850 AAATAAAAAT Statistics Matches: 24, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 8 18 0.75 9 6 0.25 ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52 Consensus pattern (8 bp): TTTAAAAT Found at i:8422 original size:33 final size:33 Alignment explanation
Indices: 8385--8489 Score: 90 Period size: 33 Copynumber: 3.2 Consensus size: 33 8375 TCAACTACAT 8385 ATATTTAAAAGTTGAAAAATATGATTCTAATCA 1 ATATTTAAAAGTTGAAAAATATGATTCTAATCA * * * * * * 8418 ATA-TTAAATAGATGAAGTGTAATAAGGTT-GAA-AA 1 ATATTTAAA-AGTTGAA---AAATATGATTCTAATCA * 8452 ATATTTAAAGGTTGAAAAATATGATTCTAATCA 1 ATATTTAAAAGTTGAAAAATATGATTCTAATCA 8485 ATATT 1 ATATT 8490 AAATAGATGA Statistics Matches: 52, Mismatches: 13, Indels: 14 0.66 0.16 0.18 Matches are distributed among these distances: 31 7 0.13 32 7 0.13 33 15 0.29 34 9 0.17 35 7 0.13 36 7 0.13 ACGTcount: A:0.48, C:0.04, G:0.13, T:0.35 Consensus pattern (33 bp): ATATTTAAAAGTTGAAAAATATGATTCTAATCA Found at i:8457 original size:67 final size:67 Alignment explanation
Indices: 8385--8523 Score: 260 Period size: 67 Copynumber: 2.1 Consensus size: 67 8375 TCAACTACAT * 8385 ATATTTAAAAGTTGAAAAATATGATTCTAATCAATATTAAATAGATGAAGTGTAATAAGGTTGAA 1 ATATTTAAAAGTTGAAAAATATGATTCTAATCAATATTAAATAGATGAAGTGTAATAAAGTTGAA 8450 AA 66 AA * 8452 ATATTTAAAGGTTGAAAAATATGATTCTAATCAATATTAAATAGATGAAGTGTAATAAAGTTGAA 1 ATATTTAAAAGTTGAAAAATATGATTCTAATCAATATTAAATAGATGAAGTGTAATAAAGTTGAA 8517 AA 66 AA 8519 ATATT 1 ATATT 8524 ATTATAATCA Statistics Matches: 70, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 67 70 1.00 ACGTcount: A:0.49, C:0.03, G:0.14, T:0.34 Consensus pattern (67 bp): ATATTTAAAAGTTGAAAAATATGATTCTAATCAATATTAAATAGATGAAGTGTAATAAAGTTGAA AA Found at i:8614 original size:16 final size:17 Alignment explanation
Indices: 8576--8614 Score: 53 Period size: 18 Copynumber: 2.3 Consensus size: 17 8566 ATTTTACTTT * 8576 TATTTTATTTTACCACTA 1 TATTTTATTTTA-CACAA 8594 TATTTTATTTTA-ACAA 1 TATTTTATTTTACACAA 8610 TATTT 1 TATTT 8615 CGGATCACTC Statistics Matches: 20, Mismatches: 1, Indels: 2 0.87 0.04 0.09 Matches are distributed among these distances: 16 8 0.40 18 12 0.60 ACGTcount: A:0.31, C:0.10, G:0.00, T:0.59 Consensus pattern (17 bp): TATTTTATTTTACACAA Found at i:13808 original size:23 final size:23 Alignment explanation
Indices: 13756--13815 Score: 59 Period size: 23 Copynumber: 2.6 Consensus size: 23 13746 TTTAATGTTC ** 13756 ACGAACATGTTCATTTAACTTAA 1 ACGAACATGTTCATCAAACTTAA * * 13779 TCAAACATGTTCA-CAAACATTAA 1 ACGAACATGTTCATCAAAC-TTAA * 13802 ACGAACATATTCAT 1 ACGAACATGTTCAT 13816 GAACATATAC Statistics Matches: 28, Mismatches: 7, Indels: 3 0.74 0.18 0.08 Matches are distributed among these distances: 22 3 0.11 23 25 0.89 ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30 Consensus pattern (23 bp): ACGAACATGTTCATCAAACTTAA Found at i:18138 original size:6 final size:6 Alignment explanation
Indices: 18127--18164 Score: 76 Period size: 6 Copynumber: 6.3 Consensus size: 6 18117 GTTTCTTGGT 18127 TGCTAA TGCTAA TGCTAA TGCTAA TGCTAA TGCTAA TG 1 TGCTAA TGCTAA TGCTAA TGCTAA TGCTAA TGCTAA TG 18165 TCATAGATGT Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 32 1.00 ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34 Consensus pattern (6 bp): TGCTAA Found at i:38200 original size:26 final size:27 Alignment explanation
Indices: 38171--38240 Score: 63 Period size: 26 Copynumber: 2.6 Consensus size: 27 38161 TTTTTTTTTG * 38171 TAAAATTAAAAGATTAAATAAATT-AT 1 TAAAATTAAAAGATTAAATAAATTAAC * * * 38197 TAAACCTTAAAA-ATAAAATAATTTAAC 1 TAAA-ATTAAAAGATTAAATAAATTAAC ** 38224 TAAAATTTGAAGATTAA 1 TAAAATTAAAAGATTAA 38241 GAGCGAGAGA Statistics Matches: 33, Mismatches: 8, Indels: 5 0.72 0.17 0.11 Matches are distributed among these distances: 26 18 0.55 27 15 0.45 ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33 Consensus pattern (27 bp): TAAAATTAAAAGATTAAATAAATTAAC Found at i:40267 original size:18 final size:19 Alignment explanation
Indices: 40193--40270 Score: 63 Period size: 20 Copynumber: 4.1 Consensus size: 19 40183 ATTACAAAAA 40193 AAAAATTCAAAATAATTT-T 1 AAAAATTCAAAAT-ATTTAT * * 40212 CAAAGCA-TCAAAATATTTTTT 1 -AAA-AATTCAAAATA-TTTAT * * 40233 TAAAATTTAAAATATTTAT 1 AAAAATTCAAAATATTTAT 40252 AAAAATTCAAAA-ATTTAT 1 AAAAATTCAAAATATTTAT 40270 A 1 A 40271 TTTTTTTAAA Statistics Matches: 47, Mismatches: 7, Indels: 10 0.73 0.11 0.16 Matches are distributed among these distances: 18 7 0.15 19 16 0.34 20 22 0.47 21 2 0.04 ACGTcount: A:0.54, C:0.06, G:0.01, T:0.38 Consensus pattern (19 bp): AAAAATTCAAAATATTTAT Found at i:40279 original size:44 final size:46 Alignment explanation
Indices: 40224--40311 Score: 128 Period size: 44 Copynumber: 1.9 Consensus size: 46 40214 AAGCATCAAA * 40224 ATATTTTTTTAAAA-TTTA-AAATATTT-ATAAAAATTCAAAAATTT 1 ATATTTTTTTAAAATTTTATAAA-ATTTAAAAAAAATTCAAAAATTT 40268 ATATTTTTTTAAAATTTTATAAAATTTAAAAAAAAATTCAAAAA 1 ATATTTTTTTAAAATTTTATAAAATTT-AAAAAAAATTCAAAAA 40312 AAACATATAA Statistics Matches: 39, Mismatches: 1, Indels: 5 0.87 0.02 0.11 Matches are distributed among these distances: 44 14 0.36 45 8 0.21 46 3 0.08 47 14 0.36 ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44 Consensus pattern (46 bp): ATATTTTTTTAAAATTTTATAAAATTTAAAAAAAATTCAAAAATTT Found at i:40299 original size:18 final size:18 Alignment explanation
Indices: 40228--40299 Score: 58 Period size: 18 Copynumber: 4.0 Consensus size: 18 40218 ATCAAAATAT * 40228 TTTTTTAAAATTT-AAAA 1 TTTTATAAAATTTAAAAA * 40245 TATTTATAAAAATTCAAAAA 1 T-TTTAT-AAAATTTAAAAA *** * 40265 -TTTATATTTTTTTAAAA 1 TTTTATAAAATTTAAAAA 40282 TTTTATAAAATTTAAAAA 1 TTTTATAAAATTTAAAAA 40300 AAAATTCAAA Statistics Matches: 40, Mismatches: 11, Indels: 7 0.69 0.19 0.12 Matches are distributed among these distances: 17 8 0.20 18 22 0.55 19 6 0.15 20 4 0.10 ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49 Consensus pattern (18 bp): TTTTATAAAATTTAAAAA Found at i:42184 original size:20 final size:21 Alignment explanation
Indices: 42149--42245 Score: 78 Period size: 21 Copynumber: 4.7 Consensus size: 21 42139 AAATAATAGT * * 42149 AAAATAACATTAAAAACAACA 1 AAAATAACAATCAAAACAACA * 42170 AAAATAACAA-CAAAAATAACACA 1 AAAATAACAATC-AAAA-CA-ACA * * 42193 AAAATAGCAATCAAAACAA-T 1 AAAATAACAATCAAAACAACA 42213 AAAA-AACAACTCAAAACAACA 1 AAAATAACAA-TCAAAACAACA 42234 AAAA-AA-AATCAA 1 AAAATAACAATCAA 42246 CCAAAATAGT Statistics Matches: 62, Mismatches: 8, Indels: 14 0.74 0.10 0.17 Matches are distributed among these distances: 19 8 0.13 20 15 0.24 21 20 0.32 22 2 0.03 23 16 0.26 24 1 0.02 ACGTcount: A:0.72, C:0.16, G:0.01, T:0.10 Consensus pattern (21 bp): AAAATAACAATCAAAACAACA Found at i:42193 original size:11 final size:12 Alignment explanation
Indices: 42107--42208 Score: 70 Period size: 12 Copynumber: 8.8 Consensus size: 12 42097 ATAACATCCA 42107 AACAACAAAAAT 1 AACAACAAAAAT * * 42119 AACAACCAAAAC 1 AACAACAAAAAT * * 42131 AGCAGCAAAAAT 1 AACAACAAAAAT * ** 42143 AA-TAGTAAAAT 1 AACAACAAAAAT ** 42154 AAC-A-TTAAA- 1 AACAACAAAAAT 42163 AACAACAAAAAT 1 AACAACAAAAAT 42175 AACAACAAAAAT 1 AACAACAAAAAT 42187 AAC-ACAAAAAT 1 AACAACAAAAAT * 42198 AGCAATCAAAA 1 AACAA-CAAAA 42209 CAATAAAAAA Statistics Matches: 69, Mismatches: 15, Indels: 11 0.73 0.16 0.12 Matches are distributed among these distances: 9 3 0.04 10 5 0.07 11 21 0.30 12 35 0.51 13 5 0.07 ACGTcount: A:0.69, C:0.17, G:0.04, T:0.11 Consensus pattern (12 bp): AACAACAAAAAT Found at i:42233 original size:23 final size:23 Alignment explanation
Indices: 42207--42251 Score: 65 Period size: 23 Copynumber: 2.0 Consensus size: 23 42197 TAGCAATCAA * 42207 AACAATAAAAAA-CAACTCAAAAC 1 AACAAAAAAAAATCAAC-CAAAAC 42230 AACAAAAAAAAATCAACCAAAA 1 AACAAAAAAAAATCAACCAAAA 42252 TAGTAAAAAA Statistics Matches: 20, Mismatches: 1, Indels: 2 0.87 0.04 0.09 Matches are distributed among these distances: 23 16 0.80 24 4 0.20 ACGTcount: A:0.73, C:0.20, G:0.00, T:0.07 Consensus pattern (23 bp): AACAAAAAAAAATCAACCAAAAC Found at i:43331 original size:23 final size:23 Alignment explanation
Indices: 43258--43429 Score: 156 Period size: 23 Copynumber: 7.5 Consensus size: 23 43248 TATACGGAAC * * 43258 AAACAGAGAGTAC-CAAAGTACT 1 AAACAGAGAGCACACAAAGTGCT * * 43280 -AACAGAGAGCACA-TAAGTGTT 1 AAACAGAGAGCACACAAAGTGCT * 43301 GGACAACAGAGAGCACACACAGTGCT 1 --A-AACAGAGAGCACACAAAGTGCT * * 43327 AAACAGAGAGTACACAAAGTACT 1 AAACAGAGAGCACACAAAGTGCT * 43350 AATCAGAGAGCACACAAAGTGCT 1 AAACAGAGAGCACACAAAGTGCT * * 43373 AATCAGAGAGCATACAAAGTGCT 1 AAACAGAGAGCACACAAAGTGCT * 43396 AATCAGAG-GC-CACAAAACGTGCT 1 AAACAGAGAGCACAC-AAA-GTGCT * 43419 AAACATAGAGC 1 AAACAGAGAGC 43430 GCGCTAGTGT Statistics Matches: 124, Mismatches: 17, Indels: 16 0.79 0.11 0.10 Matches are distributed among these distances: 21 18 0.15 22 5 0.04 23 80 0.65 24 3 0.02 25 13 0.10 26 5 0.04 ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13 Consensus pattern (23 bp): AAACAGAGAGCACACAAAGTGCT Found at i:43380 original size:69 final size:68 Alignment explanation
Indices: 43258--43403 Score: 188 Period size: 69 Copynumber: 2.1 Consensus size: 68 43248 TATACGGAAC * * * 43258 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGTTGGACAACAGAGAGCACACACAG 1 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCT-GACAACAGAGAGCACACAAAG 43323 TGCT 65 TGCT * * 43327 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT-A-ATCAGAGAGCATACAA 1 AAACAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACA-AAAGTGCTGACAACAGAGAGCACACAA 43390 AGTGCT 63 AGTGCT * 43396 AATCAGAG 1 AAACAGAG 43404 GCCACAAAAC Statistics Matches: 68, Mismatches: 6, Indels: 6 0.85 0.08 0.08 Matches are distributed among these distances: 69 39 0.57 70 12 0.18 71 11 0.16 72 6 0.09 ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14 Consensus pattern (68 bp): AAACAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCTGACAACAGAGAGCACACAAAGT GCT Found at i:54377 original size:3 final size:3 Alignment explanation
Indices: 54369--54407 Score: 69 Period size: 3 Copynumber: 13.0 Consensus size: 3 54359 TGTTAGGTTT * 54369 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA 1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA 54408 GGAGAGGGCC Statistics Matches: 34, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 3 34 1.00 ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33 Consensus pattern (3 bp): TAA Found at i:59329 original size:3 final size:3 Alignment explanation
Indices: 59316--59352 Score: 65 Period size: 3 Copynumber: 12.3 Consensus size: 3 59306 TCTTATTTTT * 59316 TCC TTC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC T 1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC T 59353 TTGCCCTAAA Statistics Matches: 32, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 3 32 1.00 ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38 Consensus pattern (3 bp): TCC Found at i:63367 original size:46 final size:46 Alignment explanation
Indices: 63314--63403 Score: 155 Period size: 46 Copynumber: 2.0 Consensus size: 46 63304 AAATGATCCA 63314 AAATCCTAATTA-TCGGATTCAAAAAATTGAATTAAGTTCAAAACTT 1 AAATCCTAATTACT-GGATTCAAAAAATTGAATTAAGTTCAAAACTT * 63360 AAATCCTAATTACTGGATTCAAAGAATTGAATTAAGTTCAAAAC 1 AAATCCTAATTACTGGATTCAAAAAATTGAATTAAGTTCAAAAC 63404 AACTCAAACT Statistics Matches: 42, Mismatches: 1, Indels: 2 0.93 0.02 0.04 Matches are distributed among these distances: 46 41 0.98 47 1 0.02 ACGTcount: A:0.46, C:0.13, G:0.10, T:0.31 Consensus pattern (46 bp): AAATCCTAATTACTGGATTCAAAAAATTGAATTAAGTTCAAAACTT Found at i:68871 original size:8 final size:8 Alignment explanation
Indices: 68858--68886 Score: 58 Period size: 8 Copynumber: 3.6 Consensus size: 8 68848 ATGTAATAGT 68858 ATTTTATA 1 ATTTTATA 68866 ATTTTATA 1 ATTTTATA 68874 ATTTTATA 1 ATTTTATA 68882 ATTTT 1 ATTTT 68887 TGAAAAGGTA Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 8 21 1.00 ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66 Consensus pattern (8 bp): ATTTTATA Found at i:69626 original size:22 final size:21 Alignment explanation
Indices: 69598--69645 Score: 71 Period size: 22 Copynumber: 2.3 Consensus size: 21 69588 TTAAAACAAA * 69598 ATTTATATTTTATTATTTTTAT 1 ATTTATATTTTA-TAATTTTAT 69620 ATTTATATTTTATAATTTTAT 1 ATTTATATTTTATAATTTTAT 69641 -TTTAT 1 ATTTAT 69646 TTAATAAATA Statistics Matches: 25, Mismatches: 1, Indels: 2 0.89 0.04 0.07 Matches are distributed among these distances: 20 5 0.20 21 8 0.32 22 12 0.48 ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71 Consensus pattern (21 bp): ATTTATATTTTATAATTTTAT Found at i:69899 original size:8 final size:7 Alignment explanation
Indices: 69870--69897 Score: 56 Period size: 7 Copynumber: 4.0 Consensus size: 7 69860 GAGCTGTTTC 69870 ATTTTTT 1 ATTTTTT 69877 ATTTTTT 1 ATTTTTT 69884 ATTTTTT 1 ATTTTTT 69891 ATTTTTT 1 ATTTTTT 69898 TAAAATATTT Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 21 1.00 ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86 Consensus pattern (7 bp): ATTTTTT Done.