Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003151.1 Kokia drynarioides strain JFW-HI SEQ_115737, 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: 43584
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Found at i:699 original size:15 final size:16
Alignment explanation
Indices: 679--708 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
669 CTTCCCTATT
679 TTCTA-TTTCTTTTAA
1 TTCTATTTTCTTTTAA
694 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
709 TTTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAA
Found at i:702 original size:22 final size:22
Alignment explanation
Indices: 674--734 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
664 TTCAACTTCC
674 CTATTTTCTATTT-CTTTTAATT
1 CTATTTTCT-TTTACTTTTAATT
*
696 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTACTTTTAATT
* *
718 CT-GTTTCTTTTATTTTT
1 CTATTTTCTTTTACTTTT
735 TCTTAGATCG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 17 0.47
22 19 0.53
ACGTcount: A:0.15, C:0.11, G:0.02, T:0.72
Consensus pattern (22 bp):
CTATTTTCTTTTACTTTTAATT
Found at i:735 original size:22 final size:22
Alignment explanation
Indices: 688--734 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
678 TTTCTATTTC
*
688 TTTTAATTCTATTTTCTTTTAT
1 TTTTAATTCTAGTTTCTTTTAT
710 TTTTAATTCT-GTTTCTTTTAT
1 TTTTAATTCTAGTTTCTTTTAT
731 TTTT
1 TTTT
735 TCTTAGATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTAATTCTAGTTTCTTTTAT
Found at i:1730 original size:18 final size:17
Alignment explanation
Indices: 1703--1741 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1693 ATTATTAATT
* *
1703 TATTTTAAATTTTAAATA
1 TATTTAAAATATTAAA-A
1721 TATTTAAAATATTAAAA
1 TATTTAAAATATTAAAA
1738 TATT
1 TATT
1742 AATATCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATTTAAAATATTAAAA
Found at i:14915 original size:22 final size:22
Alignment explanation
Indices: 14887--14930 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
14877 ATCTTATTAT
14887 TTATACTCAATGTTGCGTTTAC
1 TTATACTCAATGTTGCGTTTAC
14909 TTATACTCAATGTTGCGTTTAC
1 TTATACTCAATGTTGCGTTTAC
14931 ATGGACCGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.45
Consensus pattern (22 bp):
TTATACTCAATGTTGCGTTTAC
Found at i:15087 original size:21 final size:21
Alignment explanation
Indices: 15061--15101 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
15051 TCAAAACGAC
*
15061 ATAGTTTTGCCTTTTAACTTG
1 ATAGTTTTGACTTTTAACTTG
15082 ATAGTTTTGACTTTTAACTT
1 ATAGTTTTGACTTTTAACTT
15102 TAGAAAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.54
Consensus pattern (21 bp):
ATAGTTTTGACTTTTAACTTG
Found at i:15505 original size:19 final size:19
Alignment explanation
Indices: 15475--15544 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 19
15465 AAGAATACAA
*
15475 ATTTTAGAATTTTCATAAA-T
1 ATTTT-GAATTTT-AAAAATT
15495 ATTTTGAATTTTAAAAATT
1 ATTTTGAATTTTAAAAATT
* *
15514 ATTTTCAATTTTTGAAAATT
1 ATTTTGAA-TTTTAAAAATT
15534 ATTTTG-ATTTT
1 ATTTTGAATTTT
15545 TTTGTAATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
18 8 0.18
19 16 0.36
20 20 0.45
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.56
Consensus pattern (19 bp):
ATTTTGAATTTTAAAAATT
Found at i:15951 original size:15 final size:15
Alignment explanation
Indices: 15933--15989 Score: 78
Period size: 15 Copynumber: 3.8 Consensus size: 15
15923 GCTTGGAAGA
15933 TGCGAGCACTCATGT
1 TGCGAGCACTCATGT
* * * *
15948 TGCGAACACTGAAGC
1 TGCGAGCACTCATGT
15963 TGCGAGCACTCATGT
1 TGCGAGCACTCATGT
15978 TGCGAGCACTCA
1 TGCGAGCACTCA
15990 CATTGAGAAC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.25, C:0.28, G:0.26, T:0.21
Consensus pattern (15 bp):
TGCGAGCACTCATGT
Found at i:15967 original size:30 final size:30
Alignment explanation
Indices: 15928--15987 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
15918 TGTGAGCTTG
15928 GAAGATGCGAGCACTCATGTTGCGAACACT
1 GAAGATGCGAGCACTCATGTTGCGAACACT
* *
15958 GAAGCTGCGAGCACTCATGTTGCGAGCACT
1 GAAGATGCGAGCACTCATGTTGCGAACACT
15988 CACATTGAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.27, C:0.25, G:0.28, T:0.20
Consensus pattern (30 bp):
GAAGATGCGAGCACTCATGTTGCGAACACT
Found at i:16000 original size:45 final size:45
Alignment explanation
Indices: 15933--16018 Score: 109
Period size: 45 Copynumber: 1.9 Consensus size: 45
15923 GCTTGGAAGA
** * * *
15933 TGCGAGCACTCATGTTGCGAACACTGAAGCTGCGAGCACTCATGT
1 TGCGAGCACTCACATTGAGAACAATGAAGCTGCGAACACTCATGT
* *
15978 TGCGAGCACTCACATTGAGAACAATGATGTTGCGAACACTC
1 TGCGAGCACTCACATTGAGAACAATGAAGCTGCGAACACTC
16019 GCGTTGTGAG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 34 1.00
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (45 bp):
TGCGAGCACTCACATTGAGAACAATGAAGCTGCGAACACTCATGT
Found at i:18358 original size:20 final size:21
Alignment explanation
Indices: 18335--18381 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
18325 GAAAATGAGC
*
18335 AAAAAATAAAAGAAAT-AAAG
1 AAAAAACAAAAGAAATGAAAG
* *
18355 AAAAGACAAAAGAAATGAGAG
1 AAAAAACAAAAGAAATGAAAG
18376 AAAAAA
1 AAAAAA
18382 GAAATTGAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.77, C:0.02, G:0.15, T:0.06
Consensus pattern (21 bp):
AAAAAACAAAAGAAATGAAAG
Found at i:18383 original size:16 final size:17
Alignment explanation
Indices: 18356--18397 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
18346 GAAATAAAGA
*
18356 AAAGACAAAAGAAA-TG
1 AAAGAAAAAAGAAATTG
*
18372 AGAGAAAAAAGAAATTG
1 AAAGAAAAAAGAAATTG
18389 AAAGAAAAA
1 AAAGAAAAA
18398 TAAAAAGAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.71, C:0.02, G:0.19, T:0.07
Consensus pattern (17 bp):
AAAGAAAAAAGAAATTG
Found at i:18444 original size:99 final size:94
Alignment explanation
Indices: 18269--18446 Score: 223
Period size: 99 Copynumber: 1.8 Consensus size: 94
18259 TCTTGTAACG
* * * *
18269 AAAGAATGAGAGAAAAAGAAGTTAAAAGAAAAGAAAGACAAGAGTTGATAATGAGAGAAAATGAG
1 AAAGAATGAGAGAAAAAGAAATTAAAAAAAAAAAAAGACAAGAGTTGATAATAAGAGAAAATGAG
18334 CAAAAAATAAAAGAAATAAAGAAAAGACA
66 CAAAAAATAAAAGAAATAAAGAAAAGACA
* * *
18363 AAAGAAATGAGAGAAAAAAGAAATTGAAAGAAAAATAAAAAGAGAAGAGTTGTTGATAAGAGAAA
1 AAAG-AATGAGAG-AAAAAGAAATT-AAA-AAAAA-AAAAAGACAAGAGTTGATAATAAGAGAAA
*
18428 ATGAG-AGAAAATTAAAAGA
61 ATGAGCA-AAAAATAAAAGA
18447 GTTAGAGAGG
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
94 4 0.06
95 8 0.11
96 10 0.14
97 3 0.04
98 5 0.07
99 40 0.57
ACGTcount: A:0.64, C:0.02, G:0.22, T:0.12
Consensus pattern (94 bp):
AAAGAATGAGAGAAAAAGAAATTAAAAAAAAAAAAAGACAAGAGTTGATAATAAGAGAAAATGAG
CAAAAAATAAAAGAAATAAAGAAAAGACA
Found at i:20777 original size:15 final size:15
Alignment explanation
Indices: 20759--20858 Score: 78
Period size: 15 Copynumber: 6.7 Consensus size: 15
20749 CGGGCACTGG
20759 TGTTGCGAGCACTCA
1 TGTTGCGAGCACTCA
* *
20774 TGTTGCGAACA-TGGA
1 TGTTGCGAGCACT-CA
*
20789 -GCTGCGAGCACTCA
1 TGTTGCGAGCACTCA
20803 TGTTGCGAGCACTCA
1 TGTTGCGAGCACTCA
** * * * *
20818 CATTGAGAACAATGA
1 TGTTGCGAGCACTCA
* *
20833 TGTTGCGAACACTCG
1 TGTTGCGAGCACTCA
20848 TGTTGCGAGCA
1 TGTTGCGAGCA
20859 TGAACGAAGG
Statistics
Matches: 63, Mismatches: 19, Indels: 6
0.72 0.22 0.07
Matches are distributed among these distances:
14 10 0.16
15 53 0.84
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (15 bp):
TGTTGCGAGCACTCA
Found at i:20811 original size:44 final size:45
Alignment explanation
Indices: 20759--20858 Score: 123
Period size: 44 Copynumber: 2.2 Consensus size: 45
20749 CGGGCACTGG
** * *
20759 TGTTGCGAGCACTCATGTTGCGAAC-ATGGA-GCTGCGAGCACTCA
1 TGTTGCGAGCACTCACATTGAGAACAAT-GATGCTGCGAACACTCA
* *
20803 TGTTGCGAGCACTCACATTGAGAACAATGATGTTGCGAACACTCG
1 TGTTGCGAGCACTCACATTGAGAACAATGATGCTGCGAACACTCA
20848 TGTTGCGAGCA
1 TGTTGCGAGCA
20859 TGAACGAAGG
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
44 24 0.50
45 24 0.50
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (45 bp):
TGTTGCGAGCACTCACATTGAGAACAATGATGCTGCGAACACTCA
Found at i:22126 original size:51 final size:51
Alignment explanation
Indices: 22066--22167 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
22056 ATTACAAAAG
22066 ATAGTTCTTAATTTTGATCGGGAACTCACGCGACTCGTAATCACCTCTCGA
1 ATAGTTCTTAATTTTGATCGGGAACTCACGCGACTCGTAATCACCTCTCGA
22117 ATAGTTCTTAATTTTGATCGGGAACTCACGCGACTCGTAATCACCTCTCGA
1 ATAGTTCTTAATTTTGATCGGGAACTCACGCGACTCGTAATCACCTCTCGA
22168 GGACAAGCTC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (51 bp):
ATAGTTCTTAATTTTGATCGGGAACTCACGCGACTCGTAATCACCTCTCGA
Found at i:25526 original size:49 final size:43
Alignment explanation
Indices: 25430--25515 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
25420 AACTTAGATT
*
25430 AATTTTAGTTTAGATTGAAACTCTTCAAAATTATTATATTTCC
1 AATTTTACTTTAGATTGAAACTCTTCAAAATTATTATATTTCC
*
25473 AATTTTACTTTAGATTGAAACTCTTCAAAATTATTATAATTCC
1 AATTTTACTTTAGATTGAAACTCTTCAAAATTATTATATTTCC
25516 TTAACCAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.45
Consensus pattern (43 bp):
AATTTTACTTTAGATTGAAACTCTTCAAAATTATTATATTTCC
Found at i:37491 original size:94 final size:94
Alignment explanation
Indices: 37330--37519 Score: 362
Period size: 94 Copynumber: 2.0 Consensus size: 94
37320 CAGCTATTAA
* *
37330 CATGTCATTCACACCTTTTTTAATTAATTTTTTGACCATAATTCCTTAAAATCCCTAATTAAAAA
1 CATGTCATTCACACCTCTTTTAATTAATTTTTTGACCATAAATCCTTAAAATCCCTAATTAAAAA
37395 TTACATAACCCTAATTAAGATTTTCTCTT
66 TTACATAACCCTAATTAAGATTTTCTCTT
37424 CATGTCATTCACACCTCTTTTAATTAATTTTTTGACCATAAATCCTTAAAATCCCTAATTAAAAA
1 CATGTCATTCACACCTCTTTTAATTAATTTTTTGACCATAAATCCTTAAAATCCCTAATTAAAAA
37489 TTACATAACCCTAATTAAGATTTTCTCTT
66 TTACATAACCCTAATTAAGATTTTCTCTT
37518 CA
1 CA
37520 CGCCTTTGCT
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 94 1.00
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.41
Consensus pattern (94 bp):
CATGTCATTCACACCTCTTTTAATTAATTTTTTGACCATAAATCCTTAAAATCCCTAATTAAAAA
TTACATAACCCTAATTAAGATTTTCTCTT
Found at i:37540 original size:23 final size:22
Alignment explanation
Indices: 37508--37553 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
37498 CCTAATTAAG
37508 ATTTTCTCTTCACGCCTTTGCT
1 ATTTTCTCTTCACGCCTTTGCT
* *
37530 ATTTTGCTCTTCATGTCTTTGCT
1 ATTTT-CTCTTCACGCCTTTGCT
37553 A
1 A
37554 ATCATTGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.11, C:0.26, G:0.11, T:0.52
Consensus pattern (22 bp):
ATTTTCTCTTCACGCCTTTGCT
Found at i:43460 original size:12 final size:12
Alignment explanation
Indices: 43439--43477 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
43429 TGATCAAAAT
*
43439 TGAAAGTGAAAG
1 TGAAATTGAAAG
*
43451 TGAAATTGAAAT
1 TGAAATTGAAAG
*
43463 TGGAATTGAAAG
1 TGAAATTGAAAG
43475 TGA
1 TGA
43478 TATGAATTGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.28, T:0.26
Consensus pattern (12 bp):
TGAAATTGAAAG
Found at i:43472 original size:18 final size:17
Alignment explanation
Indices: 43435--43496 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 17
43425 TTTGTGATCA
* *
43435 AAATTGAAAGTGAAAGTG
1 AAATTGAAA-TGGAATTG
43453 AAATTGAAATTGGAATTG
1 AAATTGAAA-TGGAATTG
* *
43471 AAAGTGATAT-GAATTG
1 AAATTGAAATGGAATTG
43487 TAAATTGAAA
1 -AAATTGAAA
43497 ATCTCTATTA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
16 6 0.17
17 8 0.22
18 22 0.61
ACGTcount: A:0.48, C:0.00, G:0.23, T:0.29
Consensus pattern (17 bp):
AAATTGAAATGGAATTG
Done.