Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010475.1 Kokia drynarioides strain JFW-HI SEQ_125375, 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: 25331
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:506 original size:29 final size:29
Alignment explanation
Indices: 472--742 Score: 234
Period size: 29 Copynumber: 9.2 Consensus size: 29
462 TAAACTTTCT
472 AAAAATTACCATTTTACCCCCGAACTTCC
1 AAAAATTACCATTTTACCCCCGAACTTCC
*
501 AAAAA-T-CTCATTTTTGA-CCTCGAACCTTCC
1 AAAAATTAC-CA-TTTT-ACCCCCGAA-CTTCC
*
531 AAAAATTACCATTTTACCCTCGAACTTCC
1 AAAAATTACCATTTTACCCCCGAACTTCC
* * *
560 AAAAATCA-CATTTTTGA-CCCCAAACCTTCT
1 AAAAATTACCA-TTTT-ACCCCCGAA-CTTCC
**
590 AAAAATTACCATTTTACCCCTAAACTT-C
1 AAAAATTACCATTTTACCCCCGAACTTCC
* * * * * *
618 AAAAAATCCCATTTTTAACCTCAAACCTTTC
1 AAAAATTACCA-TTTTACCCCCGAA-CTTCC
649 AAAAATTACCATTTTACCCCCGAACTTCC
1 AAAAATTACCATTTTACCCCCGAACTTCC
* * *
678 AAAAA-TCCCATTTTTGA-CCCCAAACATTCT
1 AAAAATTACCA-TTTT-ACCCCCGAAC-TTCC
708 AAAAATTACCATTTTACCCCCGAACTTCC
1 AAAAATTACCATTTTACCCCCGAACTTCC
737 AAAAAT
1 AAAAAT
743 CCAATTTTTG
Statistics
Matches: 197, Mismatches: 25, Indels: 40
0.75 0.10 0.15
Matches are distributed among these distances:
27 1 0.01
28 18 0.09
29 81 0.41
30 77 0.39
31 19 0.10
32 1 0.01
ACGTcount: A:0.37, C:0.31, G:0.03, T:0.30
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCCCGAACTTCC
Found at i:564 original size:59 final size:59
Alignment explanation
Indices: 463--754 Score: 431
Period size: 59 Copynumber: 4.9 Consensus size: 59
453 GGAGGTCCCT
* * *
463 AAACTTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCTC
1 AAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTC
* * * *
522 GAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCACATTTTTGACCCC
1 AAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTC
* ** * *
581 AAACCTTCTAAAAATTACCATTTTACCCCTAAACTTCAAAAAATCCCATTTTTAACCTC
1 AAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTC
* *
640 AAACCTTTCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
1 AAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTC
* * *
699 AAACATTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCAATTTTTGAC
1 AAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGAC
755 TCCGAACCCC
Statistics
Matches: 207, Mismatches: 26, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 207 1.00
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.31
Consensus pattern (59 bp):
AAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTC
Found at i:3209 original size:20 final size:20
Alignment explanation
Indices: 3180--3220 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
3170 AAAAATAAGC
3180 TTTAATTATTT-TATTTTAT
1 TTTAATTATTTCTATTTTAT
*
3199 TTTACATTATTTCTCTTTTAT
1 TTTA-ATTATTTCTATTTTAT
3220 T
1 T
3221 ATTTTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
21 8 0.42
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTAATTATTTCTATTTTAT
Found at i:11656 original size:23 final size:24
Alignment explanation
Indices: 11629--11694 Score: 84
Period size: 23 Copynumber: 2.9 Consensus size: 24
11619 CTTAATGTTC
*
11629 ACGAACATGTTCATTTAAC-TTAA
1 ACGAACATGTTCATTGAACATTAA
* *
11652 TCGAATATGTTCA-TGAACATTAA
1 ACGAACATGTTCATTGAACATTAA
11675 ACGAACATGTTCA-TGAACAT
1 ACGAACATGTTCATTGAACAT
11695 ATAATTAAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 4 0.11
23 33 0.89
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (24 bp):
ACGAACATGTTCATTGAACATTAA
Found at i:13029 original size:19 final size:19
Alignment explanation
Indices: 13002--13038 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12992 CTCGTTAATG
*
13002 GTGTTTGATTAATGGAATT
1 GTGTCTGATTAATGGAATT
*
13021 GTGTCTGATTAGTGGAAT
1 GTGTCTGATTAATGGAAT
13039 CATGTGTGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.03, G:0.30, T:0.43
Consensus pattern (19 bp):
GTGTCTGATTAATGGAATT
Found at i:13355 original size:47 final size:47
Alignment explanation
Indices: 13283--13376 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 47
13273 CTTTAGTTCG
* * *
13283 ATATTAGGGAATGATAGGGTTATAGGAACCATTTATATATGTTTCTA
1 ATATTAGGGAATGATAAGGTCATAGGAACCATTTATATAGGTTTCTA
13330 ATATTAGGGAATGATAAGGTCATAGGAACCATTTATATAGGTTTCTA
1 ATATTAGGGAATGATAAGGTCATAGGAACCATTTATATAGGTTTCTA
13377 TTAGAGATCA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.35, C:0.07, G:0.21, T:0.36
Consensus pattern (47 bp):
ATATTAGGGAATGATAAGGTCATAGGAACCATTTATATAGGTTTCTA
Found at i:15883 original size:40 final size:40
Alignment explanation
Indices: 15828--16031 Score: 273
Period size: 40 Copynumber: 5.1 Consensus size: 40
15818 AAATTTCACA
** *
15828 GTATTTATTAGGCTTAATGCCTAGCAGGCTTCGTGCCGGT
1 GTATTTATCGGGCTTAGTGCCTAGCAGGCTTCGTGCCGGT
*
15868 GTATTTATCGGGCTTAGTGCCTAGCAGGTTTCGTGCCGGT
1 GTATTTATCGGGCTTAGTGCCTAGCAGGCTTCGTGCCGGT
* * **
15908 ATATTTATCGGACTTAGTGCCTAGCAAACTTCGTGCCGGT
1 GTATTTATCGGGCTTAGTGCCTAGCAGGCTTCGTGCCGGT
* * * *
15948 GTATTTATCGGGCTTAGTGCCTAGCAAGCTTCATGACGAT
1 GTATTTATCGGGCTTAGTGCCTAGCAGGCTTCGTGCCGGT
* * *
15988 GTATTTATCGGGCTTTGTGCTTAGTAGGCTTCGTGCCGGT
1 GTATTTATCGGGCTTAGTGCCTAGCAGGCTTCGTGCCGGT
16028 GTAT
1 GTAT
16032 ACTATTAGGC
Statistics
Matches: 142, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 142 1.00
ACGTcount: A:0.17, C:0.20, G:0.28, T:0.35
Consensus pattern (40 bp):
GTATTTATCGGGCTTAGTGCCTAGCAGGCTTCGTGCCGGT
Found at i:15962 original size:80 final size:80
Alignment explanation
Indices: 15840--16063 Score: 268
Period size: 80 Copynumber: 2.8 Consensus size: 80
15830 ATTTATTAGG
* *
15840 CTTAATGCCTAGCAGGCTTCGTGCCGGTGTATTTATCGGGCTTAGTGCCTAGCAGGTTTCGTGCC
1 CTTAGTGCCTAGCAGGCTTCGTGCCGGTGTATTTATCGGGCTTAGTGCCTAGCAGGTTTCGTGAC
*
15905 GGTATATTTATCGGA
66 GATATATTTATCGGA
** * * *
15920 CTTAGTGCCTAGCAAACTTCGTGCCGGTGTATTTATCGGGCTTAGTGCCTAGCAAGCTTCATGAC
1 CTTAGTGCCTAGCAGGCTTCGTGCCGGTGTATTTATCGGGCTTAGTGCCTAGCAGGTTTCGTGAC
* *
15985 GATGTATTTATCGGG
66 GATATATTTATCGGA
* * * * ** * * *
16000 CTTTGTGCTTAGTAGGCTTCGTGCCGGTGTATACTATTAGGCTTTGAGCCTAGTAGGTTTCGTG
1 CTTAGTGCCTAGCAGGCTTCGTGCCGGTGTAT-TTATCGGGCTTAGTGCCTAGCAGGTTTCGTG
16064 TCGTTTTCTT
Statistics
Matches: 119, Mismatches: 24, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
80 97 0.82
81 22 0.18
ACGTcount: A:0.17, C:0.20, G:0.28, T:0.35
Consensus pattern (80 bp):
CTTAGTGCCTAGCAGGCTTCGTGCCGGTGTATTTATCGGGCTTAGTGCCTAGCAGGTTTCGTGAC
GATATATTTATCGGA
Found at i:16497 original size:212 final size:213
Alignment explanation
Indices: 16121--16508 Score: 453
Period size: 211 Copynumber: 1.8 Consensus size: 213
16111 ATTCAAAGAC
* ** * *
16121 TTAATGTCTATATGATATGGAAAGATGAGTAAGCATATATGAAATGTAAATGGATGATAAATTAT
1 TTAATGTCTATATGATAGGGAAAGATGAGTAAGCATATACAAAATGTAAAAGAATGATAAATTAT
* * * * * * *
16186 CATGTGATGGATGAATTATGCATGGAATCCATTTCTTAATATATATTATGTTTTATGGATGTTAT
66 CATATGACGGATGAAATATGCATGGAATCCATTTCTTAATACATATAATGTTTTATGGATGCTAA
** * *
16251 GTCTACTTACTATTTATTACCATATGATTTCAATGAG-TAAGTAAGGGTTAATTGAAGGACATGT
131 GTCTACTTACTAGCTATTACCATATGAATTCAATGAGAAAAGTAAGGGTTAATTGAAGGACATGT
16315 GTAAAAACATTAATGTTA
196 GTAAAAACATTAATGTTA
* * *
16333 TTAATGT-TCATATGATAGGGAAATATGAGTATGCATATACAAAATG-AAAAGAATGA-ACATTT
1 TTAATGTCT-ATATGATAGGGAAAGATGAGTAAGCATATACAAAATGTAAAAGAATGATA-AATT
* ** * *
16395 ATCATATGACGGATGAAATATGCTTGGAATGTATTTCTTAATACATGTAATGTTTTATTGATGCT
64 ATCATATGACGGATGAAATATGCATGGAATCCATTTCTTAATACATATAATGTTTTATGGATGCT
* * **
16460 AAGTTTAAC-TATTAGCTATTAGTTATATGAATTCAATGAGAAAAGTAAG
129 AAGTCT-ACTTACTAGCTATTA-CCATATGAATTCAATGAGAAAAGTAAG
16509 TAATGCATAT
Statistics
Matches: 143, Mismatches: 28, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
210 1 0.01
211 79 0.55
212 56 0.39
213 7 0.05
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.37
Consensus pattern (213 bp):
TTAATGTCTATATGATAGGGAAAGATGAGTAAGCATATACAAAATGTAAAAGAATGATAAATTAT
CATATGACGGATGAAATATGCATGGAATCCATTTCTTAATACATATAATGTTTTATGGATGCTAA
GTCTACTTACTAGCTATTACCATATGAATTCAATGAGAAAAGTAAGGGTTAATTGAAGGACATGT
GTAAAAACATTAATGTTA
Found at i:18629 original size:21 final size:21
Alignment explanation
Indices: 18605--18656 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
18595 TGAGACAATA
18605 CTACCGATACAAGT-ATGACTT
1 CTACCGATACAAGTCATG-CTT
* *
18626 CTACCGAAACATGTCATGCTT
1 CTACCGATACAAGTCATGCTT
*
18647 CTATCGATAC
1 CTACCGATAC
18657 TAAAAATTCC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (21 bp):
CTACCGATACAAGTCATGCTT
Found at i:19511 original size:52 final size:52
Alignment explanation
Indices: 19423--19664 Score: 358
Period size: 52 Copynumber: 4.7 Consensus size: 52
19413 ATTTCGTTTA
* * * *
19423 ATACTCACGATGACACATAGTCATCGAACCTCTTAATCCGTAAAGGAATCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
* * *
19475 ATCCTCACGATGAAACATAGTCATCGGACCTTTTAATCTATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
* * *
19527 ATATTCACGATGACACATAGTCGTCAGACCTTTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
* *
19579 AAACTCACGATGACATATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
* *
19631 ATACTCACGATGACACATAGTCGTCAGACCTTTT
1 ATACTCACGATGACACATAGTCATCGGACCTTTT
19665 TTTTTTATTT
Statistics
Matches: 168, Mismatches: 22, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 168 1.00
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.29
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
Found at i:21684 original size:25 final size:25
Alignment explanation
Indices: 21655--21716 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 25
21645 TAGCAATTAA
21655 CTTTTACCTCT-TTTACAAATTACTC
1 CTTTTACCT-TATTTACAAATTACTC
*
21680 CTTTTCCCTTAGTTTACAAATTACTC
1 CTTTTACCTTA-TTTACAAATTACTC
*
21706 CTTTTCCCTTA
1 CTTTTACCTTA
21717 GTTAAGCAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 1 0.03
25 8 0.24
26 25 0.74
ACGTcount: A:0.21, C:0.29, G:0.02, T:0.48
Consensus pattern (25 bp):
CTTTTACCTTATTTACAAATTACTC
Found at i:21696 original size:26 final size:26
Alignment explanation
Indices: 21666--21719 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
21656 TTTTACCTCT
21666 TTTACAAATTACTCCTTTTCCCTTAG
1 TTTACAAATTACTCCTTTTCCCTTAG
21692 TTTACAAATTACTCCTTTTCCCTTAG
1 TTTACAAATTACTCCTTTTCCCTTAG
21718 TT
1 TT
21720 AAGCAATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.22, C:0.26, G:0.04, T:0.48
Consensus pattern (26 bp):
TTTACAAATTACTCCTTTTCCCTTAG
Found at i:23112 original size:15 final size:15
Alignment explanation
Indices: 23088--23117 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
23078 ATATTATTAA
*
23088 AAAGTTGTTACACTT
1 AAAGTAGTTACACTT
23103 AAAGTAGTTACACTT
1 AAAGTAGTTACACTT
23118 TTTCTTTTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (15 bp):
AAAGTAGTTACACTT
Found at i:23378 original size:20 final size:22
Alignment explanation
Indices: 23348--23394 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
23338 TCTCTAATTT
* *
23348 TATATTTTAAA-AAAAACATAA
1 TATAATTTAAATAAAAAAATAA
23369 -ATAATTTAAATAAAAAAATAA
1 TATAATTTAAATAAAAAAATAA
23390 TATAA
1 TATAA
23395 AAATTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 9 0.41
21 9 0.41
22 4 0.18
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (22 bp):
TATAATTTAAATAAAAAAATAA
Found at i:24566 original size:4 final size:4
Alignment explanation
Indices: 24550--24596 Score: 58
Period size: 4 Copynumber: 11.2 Consensus size: 4
24540 ACGAAAATTG
* *
24550 AAGA AAAA AAGA AAGA AAAA AGAGA AAGA AAGA AAGA AAGA GAAGA A
1 AAGA AAGA AAGA AAGA AAGA A-AGA AAGA AAGA AAGA AAGA -AAGA A
24597 GGGGAAGAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
4 30 0.81
5 7 0.19
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:24579 original size:17 final size:18
Alignment explanation
Indices: 24557--24593 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
24547 TTGAAGAAAA
24557 AAAGAAAGAAA-AAAGAG
1 AAAGAAAGAAAGAAAGAG
24574 AAAGAAAGAAAGAAAGAG
1 AAAGAAAGAAAGAAAGAG
24592 AA
1 AA
24594 GAAGGGGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (18 bp):
AAAGAAAGAAAGAAAGAG
Found at i:24596 original size:21 final size:20
Alignment explanation
Indices: 24549--24596 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 20
24539 AACGAAAATT
24549 GAAGAAAAAAAGAAAGAAAA
1 GAAGAAAAAAAGAAAGAAAA
24569 -AAGAGAAAGAAAGAAAGAAAGA
1 GAAGA-AAA-AAAGAAAGAAA-A
24591 GAAGAA
1 GAAGAA
24597 GGGGAAGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
19 4 0.17
20 3 0.12
21 11 0.46
22 2 0.08
23 4 0.17
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (20 bp):
GAAGAAAAAAAGAAAGAAAA
Found at i:24784 original size:18 final size:18
Alignment explanation
Indices: 24761--24795 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
24751 GGAAGAAATG
24761 TAAGTTTAATTAATATTT
1 TAAGTTTAATTAATATTT
*
24779 TAAGTTTAGTTAATATT
1 TAAGTTTAATTAATATT
24796 AAAATTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (18 bp):
TAAGTTTAATTAATATTT
Found at i:24995 original size:20 final size:21
Alignment explanation
Indices: 24954--24996 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
24944 TAATTTACTT
24954 TAATTTAATTTTGCTAGTTAG
1 TAATTTAATTTTGCTAGTTAG
* *
24975 TAATTTTATTTTG-TTGTTAG
1 TAATTTAATTTTGCTAGTTAG
24995 TA
1 TA
24997 GTAGTAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (21 bp):
TAATTTAATTTTGCTAGTTAG
Done.