Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: NTFQ01003174.1 Kokia drynarioides strain JFW-HI SEQ_115776, 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: 45328 ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35 Found at i:8034 original size:24 final size:24 Alignment explanation
Indices: 8007--8057 Score: 75 Period size: 24 Copynumber: 2.1 Consensus size: 24 7997 AAGATTTAAA * * 8007 ATTTATTAGCATAATATATTTGTT 1 ATTTACTAGCATAAAATATTTGTT * 8031 ATTTACTAGCATAAAATCTTTGTT 1 ATTTACTAGCATAAAATATTTGTT 8055 ATT 1 ATT 8058 ACTTTTTATA Statistics Matches: 24, Mismatches: 3, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 24 24 1.00 ACGTcount: A:0.33, C:0.08, G:0.08, T:0.51 Consensus pattern (24 bp): ATTTACTAGCATAAAATATTTGTT Found at i:10512 original size:3 final size:3 Alignment explanation
Indices: 10504--10552 Score: 75 Period size: 3 Copynumber: 16.7 Consensus size: 3 10494 AAAACACTAA 10504 AAT AAT AAT -AT AGAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT 1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT 10548 AAT AA 1 AAT AA 10553 GAGAGAAAGG Statistics Matches: 43, Mismatches: 0, Indels: 6 0.88 0.00 0.12 Matches are distributed among these distances: 2 4 0.09 3 37 0.86 4 2 0.05 ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33 Consensus pattern (3 bp): AAT Found at i:25839 original size:35 final size:35 Alignment explanation
Indices: 25793--25863 Score: 142 Period size: 35 Copynumber: 2.0 Consensus size: 35 25783 AATTTTAACA 25793 TAGTTATATTAACAATGTAGAACTGCAGGAACACG 1 TAGTTATATTAACAATGTAGAACTGCAGGAACACG 25828 TAGTTATATTAACAATGTAGAACTGCAGGAACACG 1 TAGTTATATTAACAATGTAGAACTGCAGGAACACG 25863 T 1 T 25864 CTTTAGGTCA Statistics Matches: 36, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 35 36 1.00 ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27 Consensus pattern (35 bp): TAGTTATATTAACAATGTAGAACTGCAGGAACACG Found at i:28506 original size:2 final size:2 Alignment explanation
Indices: 28499--28527 Score: 58 Period size: 2 Copynumber: 14.5 Consensus size: 2 28489 TCTGCTCCGC 28499 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T 28528 GTAGTAAAAT Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 27 1.00 ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52 Consensus pattern (2 bp): TA Found at i:31311 original size:17 final size:17 Alignment explanation
Indices: 31278--31310 Score: 59 Period size: 17 Copynumber: 2.0 Consensus size: 17 31268 AATTGTTAAA 31278 ATTGTTAAAGTTTTTTT 1 ATTGTTAAAGTTTTTTT 31295 ATTGTTAAA-TTTTTTT 1 ATTGTTAAAGTTTTTTT 31311 TGTGATATTT Statistics Matches: 16, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 16 7 0.44 17 9 0.56 ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67 Consensus pattern (17 bp): ATTGTTAAAGTTTTTTT Found at i:32675 original size:14 final size:15 Alignment explanation
Indices: 32644--32677 Score: 52 Period size: 14 Copynumber: 2.3 Consensus size: 15 32634 TTTTTATATG 32644 GAATTTTGAATTAGT 1 GAATTTTGAATTAGT * 32659 GAATTTT-AATTATT 1 GAATTTTGAATTAGT 32673 GAATT 1 GAATT 32678 AAAAGTTAGT Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 14 11 0.61 15 7 0.39 ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50 Consensus pattern (15 bp): GAATTTTGAATTAGT Found at i:34361 original size:25 final size:25 Alignment explanation
Indices: 34333--34564 Score: 252 Period size: 25 Copynumber: 9.4 Consensus size: 25 34323 CTTAAGAGAT 34333 ATATTCTGTTTGGCTCGTAAGAGCG 1 ATATTCTGTTTGGCTCGTAAGAGCG 34358 ATATTCTGTTTGGCTCGTAAGAGCG 1 ATATTCTGTTTGGCTCGTAAGAGCG * 34383 ATATTCTGTTTGGCTCGTAAGAGAG 1 ATATTCTGTTTGGCTCGTAAGAGCG * * 34408 ATATTCTGTTTGGCTTGTAAGAGTG 1 ATATTCTGTTTGGCTCGTAAGAGCG * * 34433 ATATTCTGTTTGGGTCGTAAGAGCA 1 ATATTCTGTTTGGCTCGTAAGAGCG * * * * ** 34458 ATATTTTGTCTGGCTCATAAGGGAA 1 ATATTCTGTTTGGCTCGTAAGAGCG * ** * 34483 ATATTTTGACTAGCTCGTAAGAGCG 1 ATATTCTGTTTGGCTCGTAAGAGCG *** * 34508 ATATTCTAACTGGCTCATAAGA--G 1 ATATTCTGTTTGGCTCGTAAGAGCG * * 34531 ATATTCTGTCTGGCTCGTAAGAACG 1 ATATTCTGTTTGGCTCGTAAGAGCG * 34556 TTATTCTGT 1 ATATTCTGT 34565 CTGGGCTAAT Statistics Matches: 178, Mismatches: 27, Indels: 4 0.85 0.13 0.02 Matches are distributed among these distances: 23 20 0.11 25 158 0.89 ACGTcount: A:0.24, C:0.14, G:0.25, T:0.37 Consensus pattern (25 bp): ATATTCTGTTTGGCTCGTAAGAGCG Found at i:34412 original size:75 final size:75 Alignment explanation
Indices: 34325--34552 Score: 280 Period size: 75 Copynumber: 3.1 Consensus size: 75 34315 TTCTAACTCT * 34325 TAAGAGATATATTCTGTTTGGCTCGTAAGAGCGATATTCTGTTTGGCTCGTAAGAGCGATATTCT 1 TAAGAGAAATATTCTGTTTGGCTCGTAAGAGCGATATTCTGTTTGGCTCGTAAGAGCGATATTCT * 34390 GTTTGGCTCG 66 GTCTGGCTCG * * * * * * 34400 TAAGAGAGATATTCTGTTTGGCTTGTAAGAGTGATATTCTGTTTGGGTCGTAAGAGCAATATTTT 1 TAAGAGAAATATTCTGTTTGGCTCGTAAGAGCGATATTCTGTTTGGCTCGTAAGAGCGATATTCT * 34465 GTCTGGCTCA 66 GTCTGGCTCG * * ** * *** * 34475 TAAGGGAAATATTTTGACTAGCTCGTAAGAGCGATATTCTAACTGGCTCATAAGA--GATATTCT 1 TAAGAGAAATATTCTGTTTGGCTCGTAAGAGCGATATTCTGTTTGGCTCGTAAGAGCGATATTCT 34538 GTCTGGCTCG 66 GTCTGGCTCG 34548 TAAGA 1 TAAGA 34553 ACGTTATTCT Statistics Matches: 128, Mismatches: 25, Indels: 2 0.83 0.16 0.01 Matches are distributed among these distances: 73 19 0.15 75 109 0.85 ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36 Consensus pattern (75 bp): TAAGAGAAATATTCTGTTTGGCTCGTAAGAGCGATATTCTGTTTGGCTCGTAAGAGCGATATTCT GTCTGGCTCG Found at i:34537 original size:23 final size:23 Alignment explanation
Indices: 34507--34552 Score: 65 Period size: 23 Copynumber: 2.0 Consensus size: 23 34497 TCGTAAGAGC 34507 GATATTCTAACTGGCTCATAAGA 1 GATATTCTAACTGGCTCATAAGA ** * 34530 GATATTCTGTCTGGCTCGTAAGA 1 GATATTCTAACTGGCTCATAAGA 34553 ACGTTATTCT Statistics Matches: 20, Mismatches: 3, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 23 20 1.00 ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33 Consensus pattern (23 bp): GATATTCTAACTGGCTCATAAGA Found at i:36399 original size:17 final size:17 Alignment explanation
Indices: 36377--36417 Score: 57 Period size: 17 Copynumber: 2.4 Consensus size: 17 36367 ACTCATTTTA * 36377 AAATTTATTTTAGGA-TT 1 AAATTTATTTT-GAATTT 36394 AAATTTATTTTGAATTT 1 AAATTTATTTTGAATTT 36411 AAATTTA 1 AAATTTA 36418 AATTTGTTTT Statistics Matches: 22, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 16 2 0.09 17 20 0.91 ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54 Consensus pattern (17 bp): AAATTTATTTTGAATTT Found at i:36417 original size:6 final size:6 Alignment explanation
Indices: 36392--36477 Score: 70 Period size: 6 Copynumber: 14.5 Consensus size: 6 36382 TATTTTAGGA * * ** 36392 TTAAAT TT-ATT TTGAAT TTAAAT TTAAAT TT-GTT TTAAAAT TTAAAT 1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TT-AAAT TTAAAT * * * 36439 TT-AAT TTAAGT TTAGAT TTATAT TTAAAT TTAAAAT TTA 1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TT-AAAT TTA 36478 TTATAAATAT Statistics Matches: 63, Mismatches: 12, Indels: 10 0.74 0.14 0.12 Matches are distributed among these distances: 5 12 0.19 6 42 0.67 7 9 0.14 ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55 Consensus pattern (6 bp): TTAAAT Found at i:36433 original size:24 final size:23 Alignment explanation
Indices: 36392--36470 Score: 88 Period size: 23 Copynumber: 3.4 Consensus size: 23 36382 TATTTTAGGA * 36392 TTAAATTTATTTTGAATTTAAAT 1 TTAAATTTATTTTAAATTTAAAT * 36415 TTAAATTTGTTTTAAAATTTAAAT 1 TTAAATTTATTTT-AAATTTAAAT * * * 36439 TT-AATTTAAGTTTAGATTTATAT 1 TTAAATTT-ATTTTAAATTTAAAT 36462 TTAAATTTA 1 TTAAATTTA 36471 AAATTTATTA Statistics Matches: 47, Mismatches: 6, Indels: 6 0.80 0.10 0.10 Matches are distributed among these distances: 23 28 0.60 24 19 0.40 ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56 Consensus pattern (23 bp): TTAAATTTATTTTAAATTTAAAT Found at i:36433 original size:35 final size:34 Alignment explanation
Indices: 36392--36471 Score: 90 Period size: 35 Copynumber: 2.3 Consensus size: 34 36382 TATTTTAGGA * * 36392 TTAAATTTATTTTGAATTTAAATTTAAATTTGT-T 1 TTAAATTTAATTT-AATTTAAATTTAAATTTATAT * * 36426 TTAAAATTTAAATTTAATTTAAGTTTAGATTTATAT 1 TT-AAATTT-AATTTAATTTAAATTTAAATTTATAT 36462 TTAAATTTAA 1 TTAAATTTAA 36472 AATTTATTAT Statistics Matches: 39, Mismatches: 4, Indels: 6 0.80 0.08 0.12 Matches are distributed among these distances: 34 4 0.10 35 28 0.72 36 7 0.18 ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55 Consensus pattern (34 bp): TTAAATTTAATTTAATTTAAATTTAAATTTATAT Found at i:36446 original size:18 final size:17 Alignment explanation
Indices: 36392--36477 Score: 84 Period size: 18 Copynumber: 4.9 Consensus size: 17 36382 TATTTTAGGA * 36392 TTAAATTT-ATTTTGAAT 1 TTAAATTTAAATTT-AAT ** 36409 TTAAATTTAAATTTGTT 1 TTAAATTTAAATTTAAT 36426 TTAAAATTTAAATTTAAT 1 TT-AAATTTAAATTTAAT * * 36444 TTAAGTTTAGATTTATAT 1 TTAAATTTAAATTTA-AT 36462 TTAAATTTAAAATTTA 1 TTAAATTT-AAATTTA 36478 TTATAAATAT Statistics Matches: 56, Mismatches: 9, Indels: 6 0.79 0.13 0.08 Matches are distributed among these distances: 17 22 0.39 18 28 0.50 19 6 0.11 ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55 Consensus pattern (17 bp): TTAAATTTAAATTTAAT Found at i:36484 original size:18 final size:17 Alignment explanation
Indices: 36408--36485 Score: 84 Period size: 18 Copynumber: 4.4 Consensus size: 17 36398 TTATTTTGAA * 36408 TTTAAATTTAAATTTGT 1 TTTAAATTTAAATTTAT * 36425 TTTAAAATTTAAATTTAA 1 TTT-AAATTTAAATTTAT * * 36443 TTTAAGTTTAGATTTAT 1 TTTAAATTTAAATTTAT 36460 ATTTAAATTTAAAATTTAT 1 -TTTAAATTT-AAATTTAT * 36479 TATAAAT 1 TTTAAAT 36486 ATTGAAAGTC Statistics Matches: 50, Mismatches: 8, Indels: 5 0.79 0.13 0.08 Matches are distributed among these distances: 17 14 0.28 18 29 0.58 19 7 0.14 ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54 Consensus pattern (17 bp): TTTAAATTTAAATTTAT Found at i:37195 original size:3 final size:3 Alignment explanation
Indices: 37187--37256 Score: 68 Period size: 3 Copynumber: 23.0 Consensus size: 3 37177 ATATTATCAT ** * * 37187 TAA TAA TAA TTT TAA TAA TAA TGA TAA TAT TAA TAA TAA TAAA TAA 1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA * * * 37233 CAA CAA TAA TAA TAA TAT TAA TAA 1 TAA TAA TAA TAA TAA TAA TAA TAA 37257 CATTAATTTT Statistics Matches: 54, Mismatches: 12, Indels: 2 0.79 0.18 0.03 Matches are distributed among these distances: 3 51 0.94 4 3 0.06 ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36 Consensus pattern (3 bp): TAA Found at i:37585 original size:20 final size:21 Alignment explanation
Indices: 37547--37585 Score: 62 Period size: 20 Copynumber: 1.9 Consensus size: 21 37537 AAAGGGAAAA * 37547 GTTTTAAAGGAAATCAAAATT 1 GTTTTAAAGGAAATAAAAATT 37568 GTTTTAAA-GAAATAAAAA 1 GTTTTAAAGGAAATAAAAA 37586 GAGGGATTTT Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 20 9 0.53 21 8 0.47 ACGTcount: A:0.54, C:0.03, G:0.13, T:0.31 Consensus pattern (21 bp): GTTTTAAAGGAAATAAAAATT Found at i:38445 original size:30 final size:30 Alignment explanation
Indices: 38352--38573 Score: 127 Period size: 29 Copynumber: 7.6 Consensus size: 30 38342 CACCCCGAAC * * 38352 TTCCAAAAA-T-CTATTTTTGACCC-CATTT 1 TTCCAAAAATTACCATTTTT-ACCCTAATTT * ** 38380 TCTCC-AAAATTACCA-TTTTACCCCCAA-AC 1 T-TCCAAAAATTACCATTTTTA-CCCTAATTT 38409 TTCCAAAAATT-CCATTTTTGACCCTAATTT 1 TTCCAAAAATTACCATTTTT-ACCCTAATTT * 38439 TTCCAAAAATTACCA-TTTTACCCTTGAA--C 1 TTCCAAAAATTACCATTTTTACCC-T-AATTT ** 38468 TTCCAAAAATT-CCATTTTTAACCCCGATTT 1 TTCCAAAAATTACCATTTTT-ACCCTAATTT * * 38498 CTCCAAAAATTACCA-TTTTACCCTCGAA--C 1 TTCCAAAAATTACCATTTTTACCCT--AATTT * 38527 TTCCAAAGATT-CCATTTTTTA-CCTCAATTT 1 TTCCAAAAATTACCA-TTTTTACCCT-AATTT 38557 TTCC-AAAATTACCATTT 1 TTCCAAAAATTACCATTT 38574 ACTCCTGGAT Statistics Matches: 150, Mismatches: 20, Indels: 47 0.69 0.09 0.22 Matches are distributed among these distances: 28 21 0.14 29 70 0.47 30 50 0.33 31 9 0.06 ACGTcount: A:0.32, C:0.28, G:0.03, T:0.38 Consensus pattern (30 bp): TTCCAAAAATTACCATTTTTACCCTAATTT Found at i:38456 original size:59 final size:59 Alignment explanation
Indices: 38325--38573 Score: 314 Period size: 59 Copynumber: 4.3 Consensus size: 59 38315 CCCTAAACTA * * 38325 TCCAAAAATTA-CATTTT-CACCCCGAACTTCCAAAAA-TCTATTTTTGACCC-CATTTT 1 TCCAAAAATTACCATTTTAC-CCCCGAACTTCCAAAAATTCCATTTTTGACCCTAATTTT * 38381 CTCC-AAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCCTAATTTT 1 -TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCCTAATTTT ** * ** * 38440 TCCAAAAATTACCATTTTACCCTTGAACTTCCAAAAATTCCATTTTTAACCCCGATTTC 1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCCTAATTTT * * * 38499 TCCAAAAATTACCATTTTACCCTCGAACTTCCAAAGATTCCATTTTTTA-CCTCAATTTT 1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCCT-AATTTT 38558 TCC-AAAATTACCATTT 1 TCCAAAAATTACCATTT 38574 ACTCCTGGAT Statistics Matches: 170, Mismatches: 16, Indels: 11 0.86 0.08 0.06 Matches are distributed among these distances: 56 7 0.04 57 25 0.15 58 32 0.19 59 106 0.62 ACGTcount: A:0.32, C:0.29, G:0.03, T:0.37 Consensus pattern (59 bp): TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCCTAATTTT Found at i:38545 original size:29 final size:29 Alignment explanation
Indices: 38320--38544 Score: 159 Period size: 29 Copynumber: 7.8 Consensus size: 29 38310 GAAGTCCCTA 38320 AACTATCCAAAAATTA-CATTTTCACCC-CG 1 AACT-TCCAAAAATTACCATTTT-ACCCTCG * 38349 AACTTCCAAAAATCTA--TTTTTGACCC-C- 1 AACTTCCAAAAAT-TACCATTTT-ACCCTCG ** * * * 38376 ATTTTCTCCAAAATTACCATTTTACCCCCA 1 AACTTC-CAAAAATTACCATTTTACCCTCG 38406 AACTTCCAAAAATT-CCATTTTTGACCCT-- 1 AACTTCCAAAAATTACCA-TTTT-ACCCTCG * * 38434 AATTTTTCCAAAAATTACCATTTTACCCTTG 1 AA--CTTCCAAAAATTACCATTTTACCCTCG 38465 AACTTCCAAAAATT-CCATTTTTAACCC-CG 1 AACTTCCAAAAATTACCA-TTTT-ACCCTCG ** 38494 ATTTCTCCAAAAATTACCATTTTACCCTCG 1 AACT-TCCAAAAATTACCATTTTACCCTCG * 38524 AACTTCCAAAGATT-CCATTTT 1 AACTTCCAAAAATTACCATTTT 38545 TTACCTCAAT Statistics Matches: 160, Mismatches: 18, Indels: 37 0.74 0.08 0.17 Matches are distributed among these distances: 27 6 0.04 28 43 0.27 29 58 0.36 30 45 0.28 31 8 0.05 ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35 Consensus pattern (29 bp): AACTTCCAAAAATTACCATTTTACCCTCG Found at i:41935 original size:50 final size:50 Alignment explanation
Indices: 41835--41935 Score: 141 Period size: 50 Copynumber: 2.0 Consensus size: 50 41825 CACACGAGCT * * * * 41835 GGCACACGGGCGTGTGTCTAAGCCGTGTAACTCACTATTTTGCTTGTTAA 1 GGCACACGGGCATGTGTCCAAGCCGTGTAACTCACTATTTTGCATATTAA * 41885 GGCACACGGGCATGTGTCC-AGACCGTGTAACTCACTGTTTTGCATATTAA 1 GGCACACGGGCATGTGTCCAAG-CCGTGTAACTCACTATTTTGCATATTAA 41935 G 1 G 41936 CCGAGAGTGG Statistics Matches: 45, Mismatches: 5, Indels: 2 0.87 0.10 0.04 Matches are distributed among these distances: 49 2 0.04 50 43 0.96 ACGTcount: A:0.22, C:0.23, G:0.26, T:0.30 Consensus pattern (50 bp): GGCACACGGGCATGTGTCCAAGCCGTGTAACTCACTATTTTGCATATTAA Found at i:42261 original size:59 final size:62 Alignment explanation
Indices: 42191--42308 Score: 172 Period size: 59 Copynumber: 2.0 Consensus size: 62 42181 ATCACTTTAA * * * 42191 TATTAAATTAATATAATATTTATC-A-AGAGA-AATT-TTAGATTAAATTTAATATTAAATCT 1 TATTAAATTAATAGAATATTTATCTACA-AAATAATTATTAAATTAAATTTAATATTAAATCT 42250 TATTAAATTAATAGAATATTTATCTACAAAATAATTATTAAATTAAATTTAATATTAAA 1 TATTAAATTAATAGAATATTTATCTACAAAATAATTATTAAATTAAATTTAATATTAAA 42309 ATAATCACTT Statistics Matches: 52, Mismatches: 3, Indels: 5 0.87 0.05 0.08 Matches are distributed among these distances: 59 23 0.44 60 3 0.06 61 5 0.10 62 21 0.40 ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43 Consensus pattern (62 bp): TATTAAATTAATAGAATATTTATCTACAAAATAATTATTAAATTAAATTTAATATTAAATCT Done.