Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009507.1 Kokia drynarioides strain JFW-HI SEQ_124218, 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: 63204
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33

Warning! 3 characters in sequence are not A, C, G, or T


Found at i:14458 original size:37 final size:37

Alignment explanation

Indices: 14415--14553 Score: 161 Period size: 37 Copynumber: 3.8 Consensus size: 37 14405 ATTGTTTCAA * * * 14415 TCCACTTCTCTGTAACTCATGAAGAAGATGAATTTGG 1 TCCACTTCTCTGTATCTCATCAAGAAGACGAATTTGG * * 14452 TTCACTTCTCTGTATCTCATCAAGAAGGCGAATTTGG 1 TCCACTTCTCTGTATCTCATCAAGAAGACGAATTTGG * * * * * 14489 TCCATTTCTTTGTATCTCATCAGGAAGGCGGATTTGG 1 TCCACTTCTCTGTATCTCATCAAGAAGACGAATTTGG * * * 14526 TCCACTTATTTGTATCTCATCAGGAAGA 1 TCCACTTCTCTGTATCTCATCAAGAAGA 14554 TGACCAATTT Statistics Matches: 89, Mismatches: 13, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 37 89 1.00 ACGTcount: A:0.25, C:0.20, G:0.19, T:0.35 Consensus pattern (37 bp): TCCACTTCTCTGTATCTCATCAAGAAGACGAATTTGG Found at i:14687 original size:198 final size:198 Alignment explanation

Indices: 14445--15121 Score: 737 Period size: 198 Copynumber: 3.4 Consensus size: 198 14435 GAAGAAGATG * * * * * * * 14445 AATTTGGTTCACTTCTCTGTATCTCATCAAGAAGGCGAATTTGGTCCATTTCTTTGTATCTCATC 1 AATTTGATCCACTTCTCTATATCTCATCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATC * * * * 14510 AGGAAGGCGGATTTGGTCCACTTATTTGTATCTCATCAGGAAGATGACCAATTTATTACTTTTAC 66 AGGAAGACGAATTTGGTCCACTTCTTTGTATCTCATCAGGAAGATGACCAATTTATTACTTTGAC * * * 14575 CCACTTCTTTGTATCTCATCAAGAAAATGGGGGTGCGAAGTTTCACTCACATTAAGCTTTGCTTC 131 CCACTTCTCTGTATCTCATTAAGAAAATGGGGGTGTGAAGTTTCACTCACATTAAGCTTTGCTTC 14640 ATT 196 ATT * * * 14643 AATTTGATCCACTTCTCTGTATCTCATCAGGAAGACGGATTTGGTCTACTTCTCTGTATCTCATC 1 AATTTGATCCACTTCTCTATATCTCATCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATC * * * * 14708 AAGAAGACGAATTTGGTCTACTTCTTTGTATCTCATCAGGAAGATGA-CATTTTTATTGCTTTGA 66 AGGAAGACGAATTTGGTCCACTTCTTTGTATCTCATCAGGAAGATGACCA-ATTTATTACTTTGA * * * * 14772 CCCACTTCTCTGTATCTCATTAGGAAAATGGGGTTTTGAAGTTTCACTCACATTGAGCTTTGCTT 130 CCCACTTCTCTGTATCTCATTAAGAAAATGGGGGTGTGAAGTTTCACTCACATTAAGCTTTGCTT * 14837 TATT 195 CATT * * * * * ** * 14841 GAA-TTGGTCTACATATCTAAATCTCATCAGGAAGATGACTGCCTCATTGATTTAATCCACTTTT 1 -AATTTGATCCACTTCTCTATATCTCATCAGG-A-A-GAC-G----A---ATTTGGTCCACTTCT * * * * * * * *** 14905 CTGTATCTCATTAGAAAGATGAATTTGGTTCACTTCTCTGCATCTCGTCAGGAAGATGACCGCCT 54 CTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTTTGTATCTCATCAGGAAGATGACCAATT * * * * * 14970 TATTTCTTTGACCAACTTCTCTGTATCTCATTAAGAAGATGGAGGTGTGAAGTTTTACTCACATT 119 TATTACTTTGACCCACTTCTCTGTATCTCATTAAGAAAATGGGGGTGTGAAGTTTCACTCACATT * 15035 TAGCTTTGCTTCATT 184 AAGCTTTGCTTCATT * * * * 15050 TATTTGATCCACTTCTCTATATCTCATCAGGAAGATGAATTTGGTTCACTTCTTTGTATCTCATC 1 AATTTGATCCACTTCTCTATATCTCATCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATC 15115 AGGAAGA 66 AGGAAGA 15122 TGACCACTTT Statistics Matches: 393, Mismatches: 71, Indels: 30 0.80 0.14 0.06 Matches are distributed among these distances: 197 2 0.01 198 220 0.56 199 3 0.01 200 1 0.00 201 4 0.01 202 1 0.00 205 1 0.00 206 2 0.01 207 1 0.00 208 2 0.01 209 155 0.39 210 1 0.00 ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38 Consensus pattern (198 bp): AATTTGATCCACTTCTCTATATCTCATCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATC AGGAAGACGAATTTGGTCCACTTCTTTGTATCTCATCAGGAAGATGACCAATTTATTACTTTGAC CCACTTCTCTGTATCTCATTAAGAAAATGGGGGTGTGAAGTTTCACTCACATTAAGCTTTGCTTC ATT Found at i:14694 original size:37 final size:37 Alignment explanation

Indices: 14643--14751 Score: 173 Period size: 37 Copynumber: 2.9 Consensus size: 37 14633 TTGCTTCATT * * 14643 AATTTGATCCACTTCTCTGTATCTCATCAGGAAGACG 1 AATTTGGTCTACTTCTCTGTATCTCATCAGGAAGACG * * 14680 GATTTGGTCTACTTCTCTGTATCTCATCAAGAAGACG 1 AATTTGGTCTACTTCTCTGTATCTCATCAGGAAGACG * 14717 AATTTGGTCTACTTCTTTGTATCTCATCAGGAAGA 1 AATTTGGTCTACTTCTCTGTATCTCATCAGGAAGA 14752 TGACATTTTT Statistics Matches: 65, Mismatches: 7, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 37 65 1.00 ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36 Consensus pattern (37 bp): AATTTGGTCTACTTCTCTGTATCTCATCAGGAAGACG Found at i:15076 original size:209 final size:209 Alignment explanation

Indices: 14690--15087 Score: 523 Period size: 209 Copynumber: 1.9 Consensus size: 209 14680 GATTTGGTCT * * 14690 ACTTCTCTGTATCTCATCAAGAAGACGAATTTGGTCTACTTCTTTGTATCTCATCAGGAAGATGA 1 ACTTCTCTGTATCTCATCAAGAAGACGAATTTGGTCTACTTCTCTGCATCTCATCAGGAAGATGA *** * * * 14755 CATTTTTATTGCTTTGACCCACTTCTCTGTATCTCATTAGGAAAATGGGGTTTTGAAGTTTCACT 66 CAGCCTTATTGCTTTGACCAACTTCTCTGTATCTCATTAAGAAAATGGGGTTGTGAAGTTTCACT * * * 14820 CACATTGAGCTTTGCTTTATTGAATTGGTCTACATATCTAAATCTCATCAGGAAGATGACTGCCT 131 CACATTGAGCTTTGCTTCATTGAATTGATCCACATATCTAAATCTCATCAGGAAGATGACTGCCT 14885 CATTGATTTAATCC 196 CATTGATTTAATCC * * * * 14899 ACTTTTCTGTATCTCAT-TAGAAAGATGAATTTGGT-TCACTTCTCTGCATCTCGTCAGGAAGAT 1 ACTTCTCTGTATCTCATCAAG-AAGACGAATTTGGTCT-ACTTCTCTGCATCTCATCAGGAAGAT * * * * 14962 GACCGCCTTATTTCTTTGACCAACTTCTCTGTATCTCATTAAGAAGATGGAGG-TGTGAAGTTTT 64 GACAGCCTTATTGCTTTGACCAACTTCTCTGTATCTCATTAAGAAAATGG-GGTTGTGAAGTTTC * * * * * * 15026 ACTCACATTTAGCTTTGCTTCATTTATTTGATCCACTTCTCTATATCTCATCAGGAAGATGA 128 ACTCACATTGAGCTTTGCTTCATTGAATTGATCCACATATCTAAATCTCATCAGGAAGATGA 15088 ATTTGGTTCA Statistics Matches: 161, Mismatches: 25, Indels: 6 0.84 0.13 0.03 Matches are distributed among these distances: 208 3 0.02 209 156 0.97 210 2 0.01 ACGTcount: A:0.25, C:0.20, G:0.16, T:0.38 Consensus pattern (209 bp): ACTTCTCTGTATCTCATCAAGAAGACGAATTTGGTCTACTTCTCTGCATCTCATCAGGAAGATGA CAGCCTTATTGCTTTGACCAACTTCTCTGTATCTCATTAAGAAAATGGGGTTGTGAAGTTTCACT CACATTGAGCTTTGCTTCATTGAATTGATCCACATATCTAAATCTCATCAGGAAGATGACTGCCT CATTGATTTAATCC Found at i:15092 original size:161 final size:161 Alignment explanation

Indices: 14884--15190 Score: 443 Period size: 161 Copynumber: 1.9 Consensus size: 161 14874 GATGACTGCC * * * 14884 TCATTGATTTAATCCACTTTTCTGTATCTCATTAGAAAGATGAATTTGGTTCACTTCTCTGCATC 1 TCATTGATTTAATCCACTTCTCTATATCTCATCAGAAAGATGAATTTGGTTCACTTCTCTGCATC * * * * * 14949 TCGTCAGGAAGATGACCGCCTTATTTCTTTGACCAACTTCTCTGTATCTCATTAAGAAGATGGAG 66 TCATCAGGAAGATGACCACCTTATTGCTTCGACCAACTTCTCTGTATCTCATCAAGAAGATGGAG * 15014 GTGTGAAGTTTTACTCACATTTAGCTTTGCT 131 GTGTGAAGTTTCACTCACATTTAGCTTTGCT * * * * * 15045 TCATTTATTTGATCCACTTCTCTATATCTCATCAGGAAGATGAATTTGGTTCACTTCTTTGTATC 1 TCATTGATTTAATCCACTTCTCTATATCTCATCAGAAAGATGAATTTGGTTCACTTCTCTGCATC * * * 15110 TCATCAGGAAGATGACCACTTTATTGCTTCGACCCACTTCTCTGTATCTCATCAGGAAGATGGAG 66 TCATCAGGAAGATGACCACCTTATTGCTTCGACCAACTTCTCTGTATCTCATCAAGAAGATGGAG * * 15175 TTTTGAAGTTTCACTC 131 GTGTGAAGTTTCACTC 15191 GTATTGAACT Statistics Matches: 127, Mismatches: 19, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 161 127 1.00 ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39 Consensus pattern (161 bp): TCATTGATTTAATCCACTTCTCTATATCTCATCAGAAAGATGAATTTGGTTCACTTCTCTGCATC TCATCAGGAAGATGACCACCTTATTGCTTCGACCAACTTCTCTGTATCTCATCAAGAAGATGGAG GTGTGAAGTTTCACTCACATTTAGCTTTGCT Found at i:15228 original size:161 final size:161 Alignment explanation

Indices: 14884--15246 Score: 442 Period size: 161 Copynumber: 2.3 Consensus size: 161 14874 GATGACTGCC * * * * * 14884 TCATTGATTTAATCCACTTTTCTGTATCTCATTAGAAAGATGAATTTGGTTCACTTCTCTGCATC 1 TCATTTATTTGATCCACTTCTCTATATCTCATTAGGAAGATGAATTTGGTTCACTTCTCTGCATC * * * * * 14949 TCGTCAGGAAGATGACCGCCTTATTTCTTTGACCAACTTCTCTGTATCTCATTAAGAAGATGGAG 66 TCATCAGGAAGATGACCACCTTATTGCTTCGACCAACTTCTCTGTATCTCATCAAGAAGATGGAG * * * * 15014 GTGTGAAGTTTTACTCACATTTAGCTTTGCT 131 GTGTGAAGTTTCACTCACATTGAACTTTGCA * * * 15045 TCATTTATTTGATCCACTTCTCTATATCTCATCAGGAAGATGAATTTGGTTCACTTCTTTGTATC 1 TCATTTATTTGATCCACTTCTCTATATCTCATTAGGAAGATGAATTTGGTTCACTTCTCTGCATC * * * 15110 TCATCAGGAAGATGACCACTTTATTGCTTCGACCCACTTCTCTGTATCTCATCAGGAAGATGGAG 66 TCATCAGGAAGATGACCACCTTATTGCTTCGACCAACTTCTCTGTATCTCATCAAGAAGATGGAG * * ** 15175 TTTTGAAGTTTCACTCGTATTGAACTTCT-CA 131 GTGTGAAGTTTCACTCACATTGAACTT-TGCA * ** * 15206 TCATTGT-TTTGGTCTGCTTCTCTGTATCTCATTAGGAAGAT 1 TCATT-TATTTGATCCACTTCTCTATATCTCATTAGGAAGAT 15247 AACCTTTTGA Statistics Matches: 171, Mismatches: 29, Indels: 4 0.84 0.14 0.02 Matches are distributed among these distances: 161 169 0.99 162 2 0.01 ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40 Consensus pattern (161 bp): TCATTTATTTGATCCACTTCTCTATATCTCATTAGGAAGATGAATTTGGTTCACTTCTCTGCATC TCATCAGGAAGATGACCACCTTATTGCTTCGACCAACTTCTCTGTATCTCATCAAGAAGATGGAG GTGTGAAGTTTCACTCACATTGAACTTTGCA Found at i:34507 original size:745 final size:744 Alignment explanation

Indices: 33066--34507 Score: 2161 Period size: 745 Copynumber: 1.9 Consensus size: 744 33056 GTGTTTCTGT * * * * * 33066 ATTGAAACTAGGAATGTACTATTACATCCACTACAAACCAAAAGCTAGGACCATAATATGGAGTA 1 ATTGAAACTAGGAATGTACTATTACATCAACTACAAACAAAAAACTAGCACCATAATATGGAGGA * * * * ** 33131 AGTATCATATGAATAAACCAATGTCAGCACTTGCATTATAGGTACACATATTCGTCATGCGTGTC 66 AATATCATATGAATAAACAAACGTCAGCACTTGCATTACAGACACACATATTCGTCATGCGTGTC * * * 33196 ATCCTATTTTTCTAACTTTTTTTAGTTGTATATGTTCTAGTCATGGTGACGGTAAAAAATGCACG 131 ATCCTATTTTTCTAACTTTTTGTAATTGTATATGTTCTAGTCATGGTGACAGTAAAAAATGCACG 33261 TCTATCTCCAAATTGAATGAGCTATACAAGATTTCTCTACTAGTGATATGTATGTGCCACAATGT 196 TCTATCTCCAAATTGAATGAGCTATACAAGATTTCTCTACTAGTGATATGTATGTGCCACAATGT ** * * * 33326 TGAAATAATATGCGAAGTGTAAAATTATAAAATCTTTTTGTTGTTAAACACTTTTTATGACACTT 261 TGAAATAATATGCGAAGCATAAAATCATAAAATCTTTTTGTTGTTAAACACTTTTTATCAAACTT * * * 33391 ATCACGTTTTAAAAAGGGAAATGACAACTAAATTATTGAAATTCAAAATTAATTCATACCAAATA 326 ATAACGTTTTAAAAAGGAAAATGACAACTAAATGATTGAAATTCAAAATTAATTCATACCAAATA * * * 33456 TTTCCTGCTTTGGAAATAAGCCAATGTTTCTCTTTGTCATGGGGCTACAATTCGATTATTGTATT 391 TTTCCTGCTTTGAAAATAAGCCAATGTTTCTCTTTATCATGGGACTACAATTCGATTATTGTATT * ** * * * 33521 CTTTTTTGACGTTGGCTTTTTTGGTGAATGCGTTGTCACTCAAGTTTACTAAACTGAGGATGATA 456 CTTTTTTGACGTTGACTTTTTTGGTGAACACATTGTCACCCAAGTTTACTAAACTAAGGATGATA * * * * * * 33586 GCTTTGAGTGAAATAACTAATGGAACTTGTCCAACGACAAATTCTCTTAGATAGTTAAATTTGAA 521 GCTTTAAGTGAAATAACTAATGGAACTTATCCAACGAAAAATTCTCTTAGAGAATTAAATTGGAA * * * 33651 ACAACAAATGATTTTACATTTCTACAACACTCTCGCATGCATTGCCCAAATTATGGATAGGTTTT 586 ACAACAAATGATTTTACATTTCTACAACACCCTCGAAGGCATTGCCCAAATTATGGATAGGTTTT * * * 33716 ATTTTTTTATGTAAATTTGATATTTTTTATAGTCAGAATGTAGGACGCATGCCTCAGACACATTT 651 ATTTTTTTACGTAAATTTGACATTTTTTATAGTCAGAATCTAGGACGCATGCCTCAGACACATTT 33781 TGAACAAGATTACCAGGGAAAAAACCTGC 716 TGAACAAGATTACCAGGGAAAAAACCTGC * * 33810 ATTGAAACTAGGAATGTACTATTGCATCAACTACAAACAAAAAACTAGCACCATAATTTGGAGGA 1 ATTGAAACTAGGAATGTACTATTACATCAACTACAAACAAAAAACTAGCACCATAATATGGAGGA * * * * * 33875 AATATCATATGAATGAAGAAACGTGAGCACTTGCATTACAGACACACATATTCGTTATGTGTGTC 66 AATATCATATGAATAAACAAACGTCAGCACTTGCATTACAGACACACATATTCGTCATGCGTGTC * * * 33940 ATCCTATTTTTCTTACTTTTTGTAATTGTATATGTTCTAGTCATGGTGACAGTTAAAAATGCATG 131 ATCCTATTTTTCTAACTTTTTGTAATTGTATATGTTCTAGTCATGGTGACAGTAAAAAATGCACG * * * * 34005 TGTATCTCCAAATTGGATGAGCTATACCAGATTTCTCTACTATTGATATGTATGTGCCACAATGT 196 TCTATCTCCAAATTGAATGAGCTATACAAGATTTCTCTACTAGTGATATGTATGTGCCACAATGT 34070 TGAAATAATTATGCGAAGCATAAAATCATAAAATCTTTTTGTTGTTAAA-ATCTTTTTATCAAAC 261 TGAAATAA-TATGCGAAGCATAAAATCATAAAATCTTTTTGTTGTTAAACA-CTTTTTATCAAAC * * * 34134 TTATAATGTTTTAAAAAGGAAAATGACAACTAAATGATTTAAATTCAAAATTAATTCATCCCAAA 324 TTATAACGTTTTAAAAAGGAAAATGACAACTAAATGATTGAAATTCAAAATTAATTCATACCAAA * * * * * 34199 TATTTCTTGTTTTGAAAATAAGCCAATGTTTCTCTTTATCATGGTACTACACTTTGATTATTGTA 389 TATTTCCTGCTTTGAAAATAAGCCAATGTTTCTCTTTATCATGGGACTACAATTCGATTATTGTA * * * 34264 TTTTTTATTTGATGTT-ACTTTTTTTGTGAACACATTGTCACCCAAGTTTACTAAACTAAGGATG 454 TTCTTT-TTTGACGTTGACTTTTTTGGTGAACACATTGTCACCCAAGTTTACTAAACTAAGGATG * 34328 ATAGCTTTAAGTGAAATAACTAATGGAACTTATCCAACGAAAAATTCTCTTATAGAATTAAATTG 518 ATAGCTTTAAGTGAAATAACTAATGGAACTTATCCAACGAAAAATTCTCTTAGAGAATTAAATTG * * * 34393 GAAACAACAAATGATTTTACATTTCTACAACACCCTCTAAGGCATTGCCTAATTTATGGATAGGT 583 GAAACAACAAATGATTTTACATTTCTACAACACCCTCGAAGGCATTGCCCAAATTATGGATAGGT * * 34458 TTTA-TTTTTTACGTAAATTTGACATTTTTTTATTGTGAGAATCTAGGACG 648 TTTATTTTTTTACGTAAATTTGACA-TTTTTTATAGTCAGAATCTAGGACG 34508 TATGTAATGC Statistics Matches: 620, Mismatches: 74, Indels: 7 0.88 0.11 0.01 Matches are distributed among these distances: 744 259 0.42 745 353 0.57 746 8 0.01 ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36 Consensus pattern (744 bp): ATTGAAACTAGGAATGTACTATTACATCAACTACAAACAAAAAACTAGCACCATAATATGGAGGA AATATCATATGAATAAACAAACGTCAGCACTTGCATTACAGACACACATATTCGTCATGCGTGTC ATCCTATTTTTCTAACTTTTTGTAATTGTATATGTTCTAGTCATGGTGACAGTAAAAAATGCACG TCTATCTCCAAATTGAATGAGCTATACAAGATTTCTCTACTAGTGATATGTATGTGCCACAATGT TGAAATAATATGCGAAGCATAAAATCATAAAATCTTTTTGTTGTTAAACACTTTTTATCAAACTT ATAACGTTTTAAAAAGGAAAATGACAACTAAATGATTGAAATTCAAAATTAATTCATACCAAATA TTTCCTGCTTTGAAAATAAGCCAATGTTTCTCTTTATCATGGGACTACAATTCGATTATTGTATT CTTTTTTGACGTTGACTTTTTTGGTGAACACATTGTCACCCAAGTTTACTAAACTAAGGATGATA GCTTTAAGTGAAATAACTAATGGAACTTATCCAACGAAAAATTCTCTTAGAGAATTAAATTGGAA ACAACAAATGATTTTACATTTCTACAACACCCTCGAAGGCATTGCCCAAATTATGGATAGGTTTT ATTTTTTTACGTAAATTTGACATTTTTTATAGTCAGAATCTAGGACGCATGCCTCAGACACATTT TGAACAAGATTACCAGGGAAAAAACCTGC Found at i:53357 original size:20 final size:20 Alignment explanation

Indices: 53317--53367 Score: 70 Period size: 20 Copynumber: 2.6 Consensus size: 20 53307 AAGAGAAAAA 53317 AAATT-AAAATAGAAAATTT 1 AAATTAAAAATAGAAAATTT 53336 AAATTAAAAAT-GAAAATATT 1 AAATTAAAAATAGAAAAT-TT * 53356 AAAATAAAAATA 1 AAATTAAAAATA 53368 AATAATAATA Statistics Matches: 28, Mismatches: 1, Indels: 4 0.85 0.03 0.12 Matches are distributed among these distances: 19 11 0.39 20 17 0.61 ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27 Consensus pattern (20 bp): AAATTAAAAATAGAAAATTT Found at i:62050 original size:23 final size:23 Alignment explanation

Indices: 62018--62062 Score: 81 Period size: 23 Copynumber: 2.0 Consensus size: 23 62008 CTCGTCCATA * 62018 TTGCTGACTAGACCTTCTAGAAG 1 TTGCTAACTAGACCTTCTAGAAG 62041 TTGCTAACTAGACCTTCTAGAA 1 TTGCTAACTAGACCTTCTAGAA 62063 ACTACTGACT Statistics Matches: 21, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 23 21 1.00 ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31 Consensus pattern (23 bp): TTGCTAACTAGACCTTCTAGAAG Done.