Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016254.1 Corchorus olitorius cultivar O-4 contig16287, 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: 71624
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:7410 original size:24 final size:24
Alignment explanation
Indices: 7365--7410 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
7355 CGAGCTACAA
*
7365 TTAGGGAAACACCAACATCTTCGG
1 TTAGGGAAACACCAACACCTTCGG
* *
7389 TTAGGGAAACCCCAACGCCTTC
1 TTAGGGAAACACCAACACCTTC
7411 AGTCAGGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (24 bp):
TTAGGGAAACACCAACACCTTCGG
Found at i:15714 original size:31 final size:31
Alignment explanation
Indices: 15679--15738 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
15669 AGCTTACCAA
*
15679 TTTTTCCAAATT-AAAGTACAATGGTGCTTT
1 TTTTTTCAAATTCAAAGTACAATGGTGCTTT
* * *
15709 TTTTTTGACATTCCAAGTACAATGGTGCTT
1 TTTTTTCAAATTCAAAGTACAATGGTGCTT
15739 AATACAAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 9 0.36
31 16 0.64
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (31 bp):
TTTTTTCAAATTCAAAGTACAATGGTGCTTT
Found at i:21686 original size:18 final size:18
Alignment explanation
Indices: 21663--21698 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
21653 CAGTTTTGGG
21663 GTGGAAGATCGAAAATTT
1 GTGGAAGATCGAAAATTT
21681 GTGGAAGATCGAAAATTT
1 GTGGAAGATCGAAAATTT
21699 TCACGTGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.28, T:0.28
Consensus pattern (18 bp):
GTGGAAGATCGAAAATTT
Found at i:21790 original size:29 final size:29
Alignment explanation
Indices: 21752--21841 Score: 90
Period size: 29 Copynumber: 3.0 Consensus size: 29
21742 TTGGCAAACG
*
21752 TTAGGTCCTTATTTGATCAAATTAAAAGA
1 TTAGGTCCTTATTTGACCAAATTAAAAGA
* * ** * *
21781 TTGGGTCCTTATTTGAGCATTTTGGCAAACA
1 TTAGGTCCTTATTTGACCAAATT--AAAAGA
*
21812 TTAGGCCCTTATTTGACCAAATTAAAAGA
1 TTAGGTCCTTATTTGACCAAATTAAAAGA
21841 T
1 T
21842 CATGCTCTTA
Statistics
Matches: 46, Mismatches: 13, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
29 24 0.52
31 22 0.48
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (29 bp):
TTAGGTCCTTATTTGACCAAATTAAAAGA
Found at i:21822 original size:60 final size:59
Alignment explanation
Indices: 21727--21887 Score: 216
Period size: 60 Copynumber: 2.7 Consensus size: 59
21717 GATGTCAGGT
* * * *
21727 TCTTATTTAAGTATTTTGGCAAACGTTAGGTCCTTATTTGATCAAATTAAAAGAT-TGGG
1 TCTTATTTAAGCATTTTGGCAAACGTTAGGCCCTTATTTGACCAAATTAAAAGATAT-GC
* *
21786 TCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGACCAAATTAAAAGATCATGC
1 T-CTTATTTAAGCATTTTGGCAAACGTTAGGCCCTTATTTGACCAAATTAAAAGAT-ATGC
* *
21847 TCTTATTTAAGCATTTTGGCAAACGTTAGACCCTTAATTGA
1 TCTTATTTAAGCATTTTGGCAAACGTTAGGCCCTTATTTGA
21888 ACAATTAGCC
Statistics
Matches: 89, Mismatches: 10, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
59 1 0.01
60 85 0.96
61 2 0.02
62 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (59 bp):
TCTTATTTAAGCATTTTGGCAAACGTTAGGCCCTTATTTGACCAAATTAAAAGATATGC
Found at i:21825 original size:31 final size:31
Alignment explanation
Indices: 21723--21827 Score: 97
Period size: 31 Copynumber: 3.5 Consensus size: 31
21713 AACTGATGTC
* * * *
21723 AGGTTCTTATTTAAGTATTTTGGCAAACGTT
1 AGGTCCTTATTTGAGCATTTTGGCAAACATT
* ** * *
21754 AGGTCCTTATTTGATCAAATT--AAAAGATT
1 AGGTCCTTATTTGAGCATTTTGGCAAACATT
*
21783 GGGTCCTTATTTGAGCATTTTGGCAAACATT
1 AGGTCCTTATTTGAGCATTTTGGCAAACATT
*
21814 AGGCCCTTATTTGA
1 AGGTCCTTATTTGA
21828 CCAAATTAAA
Statistics
Matches: 55, Mismatches: 17, Indels: 4
0.72 0.22 0.05
Matches are distributed among these distances:
29 22 0.40
31 33 0.60
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (31 bp):
AGGTCCTTATTTGAGCATTTTGGCAAACATT
Found at i:31963 original size:26 final size:26
Alignment explanation
Indices: 31927--31976 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
31917 TGTTTTGGAG
31927 TTTGAACCCACCCACATAAACCTTAT
1 TTTGAACCCACCCACATAAACCTTAT
31953 TTTGAACCCACCCACATAAACCTT
1 TTTGAACCCACCCACATAAACCTT
31977 TATCAGCTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.34, C:0.36, G:0.04, T:0.26
Consensus pattern (26 bp):
TTTGAACCCACCCACATAAACCTTAT
Found at i:42292 original size:16 final size:17
Alignment explanation
Indices: 42260--42293 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
42250 TTTTATTTTT
*
42260 TATTTGTTGATATATAA
1 TATTTATTGATATATAA
42277 TATTTATTGA-ATATAA
1 TATTTATTGATATATAA
42293 T
1 T
42294 TTATACGTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (17 bp):
TATTTATTGATATATAA
Found at i:42412 original size:13 final size:13
Alignment explanation
Indices: 42396--42420 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42386 ATATCATATT
42396 TTTATATTTATAA
1 TTTATATTTATAA
42409 TTTATATTTATA
1 TTTATATTTATA
42421 TAATTAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTATATTTATAA
Found at i:42434 original size:13 final size:14
Alignment explanation
Indices: 42404--42443 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
42394 TTTTTATATT
*
42404 TATAATTTATATTTA
1 TATAATTTA-ATTAA
42419 TATAA-TTAATTAA
1 TATAATTTAATTAA
42432 TATAATTTAATT
1 TATAATTTAATT
42444 TTTAAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 9 0.39
14 9 0.39
15 5 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TATAATTTAATTAA
Found at i:43757 original size:26 final size:26
Alignment explanation
Indices: 43728--43778 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
43718 TTAGTGGTAA
43728 TTTAGTGAATGGTTTTGTAATCCTTT
1 TTTAGTGAATGGTTTTGTAATCCTTT
43754 TTTAGTGAATGGTTTTGTAATCCTT
1 TTTAGTGAATGGTTTTGTAATCCTT
43779 CAACTGTCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.20, C:0.08, G:0.20, T:0.53
Consensus pattern (26 bp):
TTTAGTGAATGGTTTTGTAATCCTTT
Found at i:46530 original size:30 final size:32
Alignment explanation
Indices: 46470--46536 Score: 93
Period size: 30 Copynumber: 2.1 Consensus size: 32
46460 TTTTGATTTC
* *
46470 ATTAGAAATATTTATTAATTATATGTAATAAAT
1 ATTAGAAATATTTATT-ATAATATGCAATAAAT
46503 ATTAG-AATATTTATT-TAATATGCAATAAAT
1 ATTAGAAATATTTATTATAATATGCAATAAAT
46533 ATTA
1 ATTA
46537 TTAGAAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
30 17 0.53
32 10 0.31
33 5 0.16
ACGTcount: A:0.48, C:0.01, G:0.06, T:0.45
Consensus pattern (32 bp):
ATTAGAAATATTTATTATAATATGCAATAAAT
Found at i:49187 original size:29 final size:31
Alignment explanation
Indices: 49155--49220 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
49145 TGCAATTTGA
*
49155 GATATAACGTTAC-AAAA-CAAGCAATTAAG
1 GATATAACGTTACGAAAAGCAAGCAATCAAG
49184 GATATAACGTTACGAAAAGCAAGCAATCAAG
1 GATATAACGTTACGAAAAGCAAGCAATCAAG
49215 GATATA
1 GATATA
49221 GTCCGTTAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 13 0.38
30 4 0.12
31 17 0.50
ACGTcount: A:0.50, C:0.14, G:0.17, T:0.20
Consensus pattern (31 bp):
GATATAACGTTACGAAAAGCAAGCAATCAAG
Found at i:49387 original size:31 final size:31
Alignment explanation
Indices: 49350--49491 Score: 164
Period size: 31 Copynumber: 4.6 Consensus size: 31
49340 CCCTAACTGA
49350 TTATATCCTTAATTGCTTGAAATCGAAAACG
1 TTATATCCTTAATTGCTTGAAATCGAAAACG
* **
49381 TCATATCCTTAATTGCTTGAAATAAAAAACG
1 TTATATCCTTAATTGCTTGAAATCGAAAACG
** * *
49412 TTATATCCTTAATTGCTTG-TTTTG-TAACG
1 TTATATCCTTAATTGCTTGAAATCGAAAACG
**
49441 TTATATCCTTAATTGCTTGCGA-CAGAAAACG
1 TTATATCCTTAATTGCTTGAAATC-GAAAACG
*
49472 TTATATCCTAAATTGCTTGA
1 TTATATCCTTAATTGCTTGA
49492 TTATCATCTA
Statistics
Matches: 93, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
29 23 0.25
30 2 0.02
31 68 0.73
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (31 bp):
TTATATCCTTAATTGCTTGAAATCGAAAACG
Found at i:49456 original size:60 final size:62
Alignment explanation
Indices: 49350--49491 Score: 180
Period size: 60 Copynumber: 2.3 Consensus size: 62
49340 CCCTAACTGA
*
49350 TTATATCCTTAATTGCTTGAAATCGAAAACGTCATATCCTTAATTGCTTGAAATAAAAAACG
1 TTATATCCTTAATTGCTTGAAATCGAAAACGTCATATCCTTAATTGCTTGAAACAAAAAACG
** * * * ** *
49412 TTATATCCTTAATTGCTTG-TTTTG-TAACGTTATATCCTTAATTGCTTGCGACAGAAAACG
1 TTATATCCTTAATTGCTTGAAATCGAAAACGTCATATCCTTAATTGCTTGAAACAAAAAACG
*
49472 TTATATCCTAAATTGCTTGA
1 TTATATCCTTAATTGCTTGA
49492 TTATCATCTA
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
60 48 0.70
61 2 0.03
62 19 0.28
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (62 bp):
TTATATCCTTAATTGCTTGAAATCGAAAACGTCATATCCTTAATTGCTTGAAACAAAAAACG
Found at i:49659 original size:16 final size:16
Alignment explanation
Indices: 49622--49652 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
49612 GCATTGCTTG
49622 GTAGAAAAATGTATTA
1 GTAGAAAAATGTATTA
49638 GTAGAAAAATGTATT
1 GTAGAAAAATGTATT
49653 CTTAGAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.32
Consensus pattern (16 bp):
GTAGAAAAATGTATTA
Found at i:50555 original size:31 final size:31
Alignment explanation
Indices: 50517--50597 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 31
50507 CGTTACAAAA
* * **
50517 CAAGCAATTAAGAATGTAATGTTTTTTATTT
1 CAAGCAATTAAGAATATAAGGTTTTCGATTT
* *
50548 CAAGCAATTAAGGATATGAGGTTTTCGATTT
1 CAAGCAATTAAGAATATAAGGTTTTCGATTT
*
50579 CAAGCAATTAAGGATATAA
1 CAAGCAATTAAGAATATAA
50598 TCAGTTAGGG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (31 bp):
CAAGCAATTAAGAATATAAGGTTTTCGATTT
Found at i:50790 original size:29 final size:31
Alignment explanation
Indices: 50716--50782 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
50706 TTTAACGGAC
50716 TATATCCTTAATTGCTCGCTTTTCGTAACGT
1 TATATCCTTAATTGCTCGCTTTTCGTAACGT
*
50747 TATATCCTTAATTGCTTG-TTTT-GTAACGT
1 TATATCCTTAATTGCTCGCTTTTCGTAACGT
50776 TATATCC
1 TATATCC
50783 CAAATTGCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 14 0.40
30 4 0.11
31 17 0.49
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48
Consensus pattern (31 bp):
TATATCCTTAATTGCTCGCTTTTCGTAACGT
Found at i:59771 original size:247 final size:246
Alignment explanation
Indices: 59336--59832 Score: 922
Period size: 247 Copynumber: 2.0 Consensus size: 246
59326 CCTTCACATT
*
59336 GCAAACACTGGTTCAGTCTCTATTCCTTTTCAAAACAATTTTTTCACTTAACAGATGTCTTACAT
1 GCAAACACTGGTTCAGTCTCTATTCCTTCTCAAAACAATTTTTTCACTTAACAGATGTCTTACAT
*
59401 GTGCCAAGTGCAAATCGCAATTTAATTTCCATCTCTAAATTTTGCAAGACTAATAAAGCTTCTGT
66 GTGCCAAGTGCAAATCACAATTTAATTTCCATCTCTAAATTTTGCAAGACTAATAAAGCTTCTGT
* * *
59466 TGAATTTTTTTACTCTTATTACCTTGTGAGGGATATGCATTCGAGACAAGCACTAGCGAAAGGCT
131 TGAATTTTTTGACTCTTATTACCTTGTGAAGGATATGCATTCGAGACAAGCACTAGCGAAAGGCC
*
59531 AGAGTAGAGATGGGATCTACGAGCTCCAGTCAGCCAAGCCTGTCAGTTCTA
196 AGAGTAGAGATGGGATCTACAAGCTCCAGTCAGCCAAGCCTGTCAGTTCTA
59582 GCAAACACTGGTTCAGTCTCTATTCCTTCTCAAAACAATTCTTTTCACTTAACAGATGTCTTACA
1 GCAAACACTGGTTCAGTCTCTATTCCTTCTCAAAACAATT-TTTTCACTTAACAGATGTCTTACA
59647 TGTGCCAAGTGCAAATCACAATTTAATTTCCATCTCTAAATTTTGCAAGACTAATAAAGCTTCTG
65 TGTGCCAAGTGCAAATCACAATTTAATTTCCATCTCTAAATTTTGCAAGACTAATAAAGCTTCTG
59712 TTGAATTTTTTGACTCTTATTACCTTGTGAAGGATATGCATTCGAGACAAGCACTAGCGAAAGGC
130 TTGAATTTTTTGACTCTTATTACCTTGTGAAGGATATGCATTCGAGACAAGCACTAGCGAAAGGC
*
59777 CAGAGTAGAGATGGGATCTACAAGCTCCAGTCAGCCAAGCCTGTCATTTCTA
195 CAGAGTAGAGATGGGATCTACAAGCTCCAGTCAGCCAAGCCTGTCAGTTCTA
59829 GCAA
1 GCAA
59833 TGCTCTTGCA
Statistics
Matches: 243, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
246 39 0.16
247 204 0.84
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (246 bp):
GCAAACACTGGTTCAGTCTCTATTCCTTCTCAAAACAATTTTTTCACTTAACAGATGTCTTACAT
GTGCCAAGTGCAAATCACAATTTAATTTCCATCTCTAAATTTTGCAAGACTAATAAAGCTTCTGT
TGAATTTTTTGACTCTTATTACCTTGTGAAGGATATGCATTCGAGACAAGCACTAGCGAAAGGCC
AGAGTAGAGATGGGATCTACAAGCTCCAGTCAGCCAAGCCTGTCAGTTCTA
Done.