Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009786.1 Kokia drynarioides strain JFW-HI SEQ_124507, 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: 34053
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 5 characters in sequence are not A, C, G, or T
Found at i:326 original size:17 final size:17
Alignment explanation
Indices: 298--346 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
288 ATATATATGG
* *
298 AAATGCAATGACAATAT
1 AAATGCAGTGACAATAA
*
315 AAATGTAGTGACAATAA
1 AAATGCAGTGACAATAA
*
332 AAATGCAGGGACAAT
1 AAATGCAGTGACAAT
347 TATACTATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.51, C:0.10, G:0.18, T:0.20
Consensus pattern (17 bp):
AAATGCAGTGACAATAA
Found at i:3976 original size:470 final size:470
Alignment explanation
Indices: 3096--4034 Score: 1653
Period size: 470 Copynumber: 2.0 Consensus size: 470
3086 TGTCAAAATG
* *
3096 ATTAAATCCAAAGATAAACAGTTAAGAAGATTTGAGCATAAATCAAAATAGATCTAACATTAAGA
1 ATTAAATCCAAAGATAAACAATTAAGAAGATTTGAGCAGAAATCAAAATAGATCTAACATTAAGA
*
3161 GGTATTTCCATACACAATTAAAGTCATCAGAATTTATCAATGTTTAAGAGGAATTAAAGAATAAG
66 GGTATTTCCATACACAATTAAAGTCATCAGAATTTATCAACGTTTAAGAGGAATTAAAGAATAAG
* * *
3226 TTGAAGCACTCTATTCCTAGCCTACTAGAACTATACCATAAATGCTCCTCTTGTGTCGCACTTAG
131 TTGAAACACTCTATTCCTAGCATACTAGAACTATACCATAAATGCTCCTCTTGTGTCGCACTAAG
*
3291 AACACTCCTCGTCAGGAGTAGATGCTGCCCTCTCATCAACATCAGGTTCCTCCGAATGGTCTCAA
196 AACACTCCTCATCAGGAGTAGATGCTGCCCTCTCATCAACATCAGGTTCCTCCGAATGGTCTCAA
*
3356 GCCTCCATAGCCCAAAAGCTCACAAGCTAGGTTGAAGAAGATAATATTGCAAAATGGGAGACTAA
261 GCCTCCATAGCCCAAAAGCTCACAAGCTAGGTTGAAGAAGATAATATTGCAAAATGGGAAACTAA
*
3421 AGGAAGAAGAGACACCTTTCTCTTTCCTTGTGAGTGTTTATATTTAGCCCAAATTGTACAAGTGT
326 AGGAAGAAGAGACACCTTTCTCTTTCCTTGTGAGTGTTCATATTTAGCCCAAATTGTACAAGTGT
3486 CTATTCTGCAAAATTGAGCTGTACAAGTTGGTTATACAAAATTGGATAGCTCACACATTTTTGTT
391 CTATTCTGCAAAATTGAGCTGTACAAGTTGGTTATACAAAATTGGATAGCTCACACATTTTTGTT
3551 CTTATTAGACAGCTA
456 CTTATTAGACAGCTA
*
3566 ATTAAATCCAAAGATAAACAATTAAGAAGATTTGAGCAGAAATCAAAATAGATTTAACATTAAGA
1 ATTAAATCCAAAGATAAACAATTAAGAAGATTTGAGCAGAAATCAAAATAGATCTAACATTAAGA
*
3631 GGTATTTCCATACACAATTAAAGTCATCAGAATTTATCAACGTTTGAGAGGAATTAAAGAATAAG
66 GGTATTTCCATACACAATTAAAGTCATCAGAATTTATCAACGTTTAAGAGGAATTAAAGAATAAG
* * * *
3696 TTGAAACATTCTATTCCTAGCATACTAGAACTATTCCGTAAATGCTCCTTTTGTGTCGCACTAAG
131 TTGAAACACTCTATTCCTAGCATACTAGAACTATACCATAAATGCTCCTCTTGTGTCGCACTAAG
* *
3761 AACACTCCTCATCAGGAGTAGATGCTTCCTTCTCATCAACATCAGGTTCCTCCGAATGGTCTCAA
196 AACACTCCTCATCAGGAGTAGATGCTGCCCTCTCATCAACATCAGGTTCCTCCGAATGGTCTCAA
*
3826 GCTTCCATAGCCCAAAAGCTCACAAGCTAGGTTGAAGAAGATAATATTGCAAAATGGGAAACTAA
261 GCCTCCATAGCCCAAAAGCTCACAAGCTAGGTTGAAGAAGATAATATTGCAAAATGGGAAACTAA
*
3891 AGGAAGAAGAGACACCTTTCTCTTTCCTTGTGAGTGTTCATATTTAGCCCAAATTGTACAGGTGT
326 AGGAAGAAGAGACACCTTTCTCTTTCCTTGTGAGTGTTCATATTTAGCCCAAATTGTACAAGTGT
* * * * * *
3956 TTATTCTGTAAAATTGAGCTGTTCAAGTTGGTTATACAAGATTGGATAGGTCATACATTTTTGTT
391 CTATTCTGCAAAATTGAGCTGTACAAGTTGGTTATACAAAATTGGATAGCTCACACATTTTTGTT
4021 CTTATTAGACAGCT
456 CTTATTAGACAGCT
4035 GTTAGATGCG
Statistics
Matches: 444, Mismatches: 25, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
470 444 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (470 bp):
ATTAAATCCAAAGATAAACAATTAAGAAGATTTGAGCAGAAATCAAAATAGATCTAACATTAAGA
GGTATTTCCATACACAATTAAAGTCATCAGAATTTATCAACGTTTAAGAGGAATTAAAGAATAAG
TTGAAACACTCTATTCCTAGCATACTAGAACTATACCATAAATGCTCCTCTTGTGTCGCACTAAG
AACACTCCTCATCAGGAGTAGATGCTGCCCTCTCATCAACATCAGGTTCCTCCGAATGGTCTCAA
GCCTCCATAGCCCAAAAGCTCACAAGCTAGGTTGAAGAAGATAATATTGCAAAATGGGAAACTAA
AGGAAGAAGAGACACCTTTCTCTTTCCTTGTGAGTGTTCATATTTAGCCCAAATTGTACAAGTGT
CTATTCTGCAAAATTGAGCTGTACAAGTTGGTTATACAAAATTGGATAGCTCACACATTTTTGTT
CTTATTAGACAGCTA
Found at i:4300 original size:37 final size:37
Alignment explanation
Indices: 4223--4293 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
4213 TTCTTGCGGT
* *
4223 GACAGTTTTGGGTGTAATCTGGAAGTGCTCATGCGAC
1 GACAGTTTTGGGTGCAATCTAGAAGTGCTCATGCGAC
*
4260 GACAGTTTTGGGCT-CAATCTAGAAGTTCTCATGC
1 GACAGTTTTGGG-TGCAATCTAGAAGTGCTCATGC
4294 AGCGACATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
37 29 0.97
38 1 0.03
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (37 bp):
GACAGTTTTGGGTGCAATCTAGAAGTGCTCATGCGAC
Found at i:8213 original size:2 final size:2
Alignment explanation
Indices: 8206--8230 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8196 TATATCCATA
8206 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
8231 AAAAAGAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8366 original size:24 final size:22
Alignment explanation
Indices: 8339--8386 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 22
8329 AGTAAAATAG
*
8339 AAATAGTGATAATTATATATTTAA
1 AAATAATGATAATT-TA-ATTTAA
*
8363 AAATAATTATAATTTAATTTAA
1 AAATAATGATAATTTAATTTAA
8385 AA
1 AA
8387 TTATTAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 8 0.36
23 2 0.09
24 12 0.55
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (22 bp):
AAATAATGATAATTTAATTTAA
Found at i:10581 original size:4 final size:4
Alignment explanation
Indices: 10561--10596 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
10551 TTCATTATTT
* *
10561 TTAA TTAA TAAA ATAA TTAA TTAA TTAA TTAA TTAA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA
10597 AACTAAAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (4 bp):
TTAA
Found at i:10772 original size:26 final size:26
Alignment explanation
Indices: 10736--10799 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
10726 AAATATTTGG
* *
10736 CAAGTATCAAATCGAA-CAAAAAAATT
1 CAAGTACCAAAT-GAAGAAAAAAAATT
* *
10762 TAAGTACCAAATTAAGAAAAAAAATT
1 CAAGTACCAAATGAAGAAAAAAAATT
10788 CAAGTACCAAAT
1 CAAGTACCAAAT
10800 TGGACCTCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 2 0.06
26 30 0.94
ACGTcount: A:0.58, C:0.14, G:0.08, T:0.20
Consensus pattern (26 bp):
CAAGTACCAAATGAAGAAAAAAAATT
Found at i:10833 original size:22 final size:21
Alignment explanation
Indices: 10808--10855 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
10798 ATTGGACCTC
* *
10808 AAAAAGTTTAAATATCAATTT
1 AAAAAATTTAAATATCAAATT
**
10829 AAAAAATTTAGGTATCAAATT
1 AAAAAATTTAAATATCAAATT
10850 AAAAAA
1 AAAAAA
10856 ATCAAATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.31
Consensus pattern (21 bp):
AAAAAATTTAAATATCAAATT
Found at i:10861 original size:14 final size:15
Alignment explanation
Indices: 10842--10871 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
10832 AAATTTAGGT
10842 ATCAAA-TTAAAAAA
1 ATCAAATTTAAAAAA
10856 ATCAAATTTAAAAAA
1 ATCAAATTTAAAAAA
10871 A
1 A
10872 AATAATTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (15 bp):
ATCAAATTTAAAAAA
Found at i:10870 original size:37 final size:36
Alignment explanation
Indices: 10824--10894 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 36
10814 TTTAAATATC
** * *
10824 AATTTAAAAAATTTAGGTATCAAATTAAAAAAATCA
1 AATTTAAAAAAAATAAGTATCAAAATAAAAAAATCA
*
10860 AATTTAAAAAAAAATAATTATCAAAATAAAAAAAT
1 AATTT-AAAAAAAATAAGTATCAAAATAAAAAAAT
10895 TGTCAAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
36 5 0.17
37 24 0.83
ACGTcount: A:0.65, C:0.04, G:0.03, T:0.28
Consensus pattern (36 bp):
AATTTAAAAAAAATAAGTATCAAAATAAAAAAATCA
Found at i:10901 original size:40 final size:37
Alignment explanation
Indices: 10841--10920 Score: 99
Period size: 40 Copynumber: 2.1 Consensus size: 37
10831 AAAATTTAGG
*
10841 TATCAAATTAAAAAAATCAAATTTAAA-AAAAAATAAT
1 TATCAAAATAAAAAAATCAAATTTAAATAAAAAAT-AT
*
10878 TATCAAAATAAAAAAATTGTCAAATTTAAATACAAAATAT
1 TATCAAAATAAAAAAA---TCAAATTTAAATAAAAAATAT
10918 TAT
1 TAT
10921 ATTAATCCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
37 15 0.41
40 16 0.43
41 6 0.16
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.30
Consensus pattern (37 bp):
TATCAAAATAAAAAAATCAAATTTAAATAAAAAATAT
Found at i:16579 original size:16 final size:18
Alignment explanation
Indices: 16558--16590 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16548 TTAAACACAA
16558 AATTAA-AC-AAATTTAC
1 AATTAACACTAAATTTAC
16574 AATTAACACTAAATTTA
1 AATTAACACTAAATTTA
16591 TTCTGTTGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (18 bp):
AATTAACACTAAATTTAC
Found at i:17734 original size:448 final size:448
Alignment explanation
Indices: 16899--17795 Score: 1776
Period size: 448 Copynumber: 2.0 Consensus size: 448
16889 GCCCAATTTT
16899 ATTCAGTTATTACATAAAATAATTAATTTACACATTTAACAACAAACAAAGAAGAGCCATGATTT
1 ATTCAGTTATTACATAAAATAATTAATTTACACATTTAACAACAAACAAAGAAGAGCCATGATTT
16964 GTAAGTAGCCAGAGACATGGTATGCGCAAAGAATTTCATTCTATTATCAGATAAACTAATTAATT
66 GTAAGTAGCCAGAGACATGGTATGCGCAAAGAATTTCATTCTATTATCAGATAAACTAATTAATT
17029 AATATAAACAAGTATTTGTCACCTAAATTGCTTGCATTCTCTTCTTTCAAATATCATAGATGTCC
131 AATATAAACAAGTATTTGTCACCTAAATTGCTTGCATTCTCTTCTTTCAAATATCATAGATGTCC
17094 AAGTTAGTTTCCACCTTACTAATAGGCCTTTCATTTGGAAAAAAGACACTAAAGAATATAGAATG
196 AAGTTAGTTTCCACCTTACTAATAGGCCTTTCATTTGGAAAAAAGACACTAAAGAATATAGAATG
17159 AATACAATTTGCAATATTTAAGATAATTCCTACATCACAAGAAAAGACACTTCCTACCATTAACA
261 AATACAATTTGCAATATTTAAGATAATTCCTACATCACAAGAAAAGACACTTCCTACCATTAACA
*
17224 GTTCAAGATAGAATTGGATTTGACACAATAGAATGGAAGTCTACTGAGATATTCAAAGAAAAAAC
326 GTTCAAGATAGAATTGGATTTGACACAATAGAATGGAAGTCTAATGAGATATTCAAAGAAAAAAC
17289 TGTAAATGATTAAGAAAAACAGTTTTCTTTCTTCAGTTATTACAGGCTTATCTTTTAG
391 TGTAAATGATTAAGAAAAACAGTTTTCTTTCTTCAGTTATTACAGGCTTATCTTTTAG
*
17347 ATTCAGTTATTACATAAAGTAATTAATTTACACATTTAACAACAAACAAAGAAGAGCCATGATTT
1 ATTCAGTTATTACATAAAATAATTAATTTACACATTTAACAACAAACAAAGAAGAGCCATGATTT
17412 GTAAGTAGCCAGAGACATGGTATGCGCAAAGAATTTCATTCTATTATCAGATAAACTAATTAATT
66 GTAAGTAGCCAGAGACATGGTATGCGCAAAGAATTTCATTCTATTATCAGATAAACTAATTAATT
17477 AATATAAACAAGTATTTGTCACCTAAATTGCTTGCATTCTCTTCTTTCAAATATCATAGATGTCC
131 AATATAAACAAGTATTTGTCACCTAAATTGCTTGCATTCTCTTCTTTCAAATATCATAGATGTCC
17542 AAGTTAGTTTCCACCTTACTAATAGGCCTTTCATTTGGAAAAAAGACACTAAAGAATATAGAATG
196 AAGTTAGTTTCCACCTTACTAATAGGCCTTTCATTTGGAAAAAAGACACTAAAGAATATAGAATG
17607 AATACAATTTGCAATATTTAAGATAATTCCTACATCACAAGAAAAGACACTTCCTACCATTAACA
261 AATACAATTTGCAATATTTAAGATAATTCCTACATCACAAGAAAAGACACTTCCTACCATTAACA
17672 GTTCAAGATAGAATTGGATTTGACACAATAGAATGGAAGTCTAATGAGATATTCAAAGAAAAAAC
326 GTTCAAGATAGAATTGGATTTGACACAATAGAATGGAAGTCTAATGAGATATTCAAAGAAAAAAC
17737 TGTAAATGATTAAGAAAAACAGTTTTCTTTCTTCAGTTATTACAGGCTTATCTTTTAG
391 TGTAAATGATTAAGAAAAACAGTTTTCTTTCTTCAGTTATTACAGGCTTATCTTTTAG
17795 A
1 A
17796 ATATCTGTCA
Statistics
Matches: 447, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
448 447 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (448 bp):
ATTCAGTTATTACATAAAATAATTAATTTACACATTTAACAACAAACAAAGAAGAGCCATGATTT
GTAAGTAGCCAGAGACATGGTATGCGCAAAGAATTTCATTCTATTATCAGATAAACTAATTAATT
AATATAAACAAGTATTTGTCACCTAAATTGCTTGCATTCTCTTCTTTCAAATATCATAGATGTCC
AAGTTAGTTTCCACCTTACTAATAGGCCTTTCATTTGGAAAAAAGACACTAAAGAATATAGAATG
AATACAATTTGCAATATTTAAGATAATTCCTACATCACAAGAAAAGACACTTCCTACCATTAACA
GTTCAAGATAGAATTGGATTTGACACAATAGAATGGAAGTCTAATGAGATATTCAAAGAAAAAAC
TGTAAATGATTAAGAAAAACAGTTTTCTTTCTTCAGTTATTACAGGCTTATCTTTTAG
Found at i:28541 original size:30 final size:30
Alignment explanation
Indices: 28507--28566 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
28497 AGAGAAAAAG
28507 CGTCCA-CTTAAACGAACTTTTCAGAAAGCT
1 CGTCCAGC-TAAACGAACTTTTCAGAAAGCT
* **
28537 CGTCCAGCTAAATGTGCTTTTCAGAAAGCT
1 CGTCCAGCTAAACGAACTTTTCAGAAAGCT
28567 TGCCTAGCTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (30 bp):
CGTCCAGCTAAACGAACTTTTCAGAAAGCT
Found at i:29717 original size:14 final size:15
Alignment explanation
Indices: 29693--29721 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
29683 TTATCTTTTC
29693 TTTGTTTCATCATCA
1 TTTGTTTCATCATCA
29708 TTTG-TTCATCATCA
1 TTTGTTTCATCATCA
29722 CCAGTATCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.52
Consensus pattern (15 bp):
TTTGTTTCATCATCA
Found at i:33031 original size:158 final size:158
Alignment explanation
Indices: 32743--33064 Score: 536
Period size: 158 Copynumber: 2.0 Consensus size: 158
32733 ATTTCGGGAT
* * *
32743 TTACAGGTTATATGGGTGCTAGTCTTAGATGTCCTACCGATGGCTGAGATTCGACATATGTTGCG
1 TTACATGTTATATGGGTGCTAGTCTTAGATGTCCTACAGATGGCTGAGATCCGACATATGTTGCG
*
32808 GATTCTCCACAGCTCATGTGAGCAGCATCGTGTAGCCTAACATCTTGACCCACAACTCATGTGAG
66 GATTCTCCACAGCTCATGTGAGCAGCATCGTGTAGCCTAACATCATGACCCACAACTCATGTGAG
*
32873 CAGACCCATTTCACAGCTCGTGTGAGCA
131 CAGACCCATTTCACAGCTCATGTGAGCA
*
32901 TTACATGTTATATGGGTGCTAGTCTTAGATGTCCTACAGATGGCTGAGATCCGGCATATGTTGCG
1 TTACATGTTATATGGGTGCTAGTCTTAGATGTCCTACAGATGGCTGAGATCCGACATATGTTGCG
* * *
32966 GATTCTCCACAGCTCGTGTGAGCAGCATCGTGTAGCCTAACATCATGACCCACAGCTCGTGTGAG
66 GATTCTCCACAGCTCATGTGAGCAGCATCGTGTAGCCTAACATCATGACCCACAACTCATGTGAG
* *
33031 CAGACCCATTTTACAGCTTATGTGAGCA
131 CAGACCCATTTCACAGCTCATGTGAGCA
*
33059 CTACAT
1 TTACAT
33065 AATACAGAGA
Statistics
Matches: 152, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
158 152 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (158 bp):
TTACATGTTATATGGGTGCTAGTCTTAGATGTCCTACAGATGGCTGAGATCCGACATATGTTGCG
GATTCTCCACAGCTCATGTGAGCAGCATCGTGTAGCCTAACATCATGACCCACAACTCATGTGAG
CAGACCCATTTCACAGCTCATGTGAGCA
Done.