Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016226.1 Corchorus capsularis cultivar CVL-1 contig16247, 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: 40804
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:4446 original size:1 final size:1
Alignment explanation
Indices: 4440--4579 Score: 100
Period size: 1 Copynumber: 140.0 Consensus size: 1
4430 GTGTAAGGTT
* * ** * * * *
4440 AAAAAAAAAAACAAAAAACAAAAAAACCAAAAACAAAAAAAAACAAAAAAACAAAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * ** * * * * *
4505 AAAAAGAGAAAAAGAAGAAAAAAACCAAAAAAAAAAAACAAAAAAAACAAAAAAAAGAGAAAAAG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
4570 AGAAAAAAAA
1 AAAAAAAAAA
4580 GAAGAAAGGA
Statistics
Matches: 103, Mismatches: 36, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 103 1.00
ACGTcount: A:0.86, C:0.09, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:4457 original size:8 final size:8
Alignment explanation
Indices: 4440--4559 Score: 119
Period size: 8 Copynumber: 15.5 Consensus size: 8
4430 GTGTAAGGTT
4440 AAAA-AAA
1 AAAACAAA
4447 AAAAC-AA
1 AAAACAAA
4454 AAAACAAA
1 AAAACAAA
4462 AAAACCAAA
1 AAAA-CAAA
4471 AACAA-AAA
1 AA-AACAAA
4479 AAAACAAA
1 AAAACAAA
4487 AAAACAAA
1 AAAACAAA
4495 AAAACAAA
1 AAAACAAA
4503 AAAA-AAA
1 AAAACAAA
* *
4510 GAGA-AAA
1 AAAACAAA
* *
4517 AGAAGAAA
1 AAAACAAA
*
4525 AAAAC-CA
1 AAAACAAA
4532 AAAA-AAA
1 AAAACAAA
4539 AAAACAAAA
1 AAAAC-AAA
4548 AAAACAAA
1 AAAACAAA
4556 AAAA
1 AAAA
4560 AGAGAAAAAG
Statistics
Matches: 95, Mismatches: 9, Indels: 17
0.79 0.07 0.14
Matches are distributed among these distances:
7 32 0.34
8 47 0.49
9 14 0.15
10 2 0.02
ACGTcount: A:0.87, C:0.10, G:0.03, T:0.00
Consensus pattern (8 bp):
AAAACAAA
Found at i:4507 original size:44 final size:45
Alignment explanation
Indices: 4440--4551 Score: 138
Period size: 44 Copynumber: 2.4 Consensus size: 45
4430 GTGTAAGGTT
*
4440 AAAAAAAAAAACAAAAAACAAAAAAACCAAAAACAA-AAAAAAACAAA
1 AAAAAAAAAAAC-AAAAA-AAAAAGA-CAAAAACAAGAAAAAAACAAA
* * *
4487 AAAACAAAAAAACAAAAAAAAAAGAGAAAAAGAAGAAAAAAAC-CA
1 AAAA-AAAAAAACAAAAAAAAAAGACAAAAACAAGAAAAAAACAAA
4532 AAAAAAAAAAACAAAAAAAA
1 AAAAAAAAAAACAAAAAAAA
4552 CAAAAAAAAG
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
44 16 0.27
45 12 0.20
46 14 0.24
47 9 0.15
48 8 0.14
ACGTcount: A:0.87, C:0.10, G:0.04, T:0.00
Consensus pattern (45 bp):
AAAAAAAAAAACAAAAAAAAAAGACAAAAACAAGAAAAAAACAAA
Found at i:4535 original size:70 final size:72
Alignment explanation
Indices: 4452--4586 Score: 179
Period size: 70 Copynumber: 1.9 Consensus size: 72
4442 AAAAAAAAAC
**
4452 AAAAAACAAAAAAACCAAAAACAAAAAAAAACAAAAAAACA-A-AAAAACAAAAAAAAAAG-AGA
1 AAAAAACAAAAAAAAAAAAAAC-AAAAAAAACAAAAAAA-AGAGAAAAACAAAAAAAAAAGAAGA
4514 AAAAGAAGA
64 AAAAGAAGA
* * *
4523 AAAAAAC-CAAAAAAAAAAAACAAAAAAAACAAAAAAAAGAGAAAAAGAGAAAAAAAAGAAGAAA
1 AAAAAACAAAAAAAAAAAAAACAAAAAAAACAAAAAAAAGAGAAAAACAAAAAAAAAAGAAGAAA
4587 GGAATAAAAG
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
68 1 0.02
69 17 0.30
70 26 0.46
71 12 0.21
ACGTcount: A:0.84, C:0.08, G:0.07, T:0.00
Consensus pattern (72 bp):
AAAAAACAAAAAAAAAAAAAACAAAAAAAACAAAAAAAAGAGAAAAACAAAAAAAAAAGAAGAAA
AAGAAGA
Found at i:4579 original size:51 final size:53
Alignment explanation
Indices: 4478--4578 Score: 172
Period size: 51 Copynumber: 2.0 Consensus size: 53
4468 AAAAACAAAA
4478 AAAAACAAAAAAACAAAAAAACAAAAAAAAAAGAGAAAAAGAAGAAAAAAACC
1 AAAAACAAAAAAACAAAAAAACAAAAAAAAAAGAGAAAAAGAAGAAAAAAACC
*
4531 AAAAA-AAAAAAACAAAAAAA-ACAAAAAAAAGAGAAAAAG-AGAAAAAAA
1 AAAAACAAAAAAACAAAAAAACAAAAAAAAAAGAGAAAAAGAAGAAAAAAA
4579 AGAAGAAAGG
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
50 9 0.19
51 18 0.38
52 15 0.32
53 5 0.11
ACGTcount: A:0.85, C:0.07, G:0.08, T:0.00
Consensus pattern (53 bp):
AAAAACAAAAAAACAAAAAAACAAAAAAAAAAGAGAAAAAGAAGAAAAAAACC
Found at i:5549 original size:35 final size:35
Alignment explanation
Indices: 5510--5806 Score: 418
Period size: 35 Copynumber: 8.5 Consensus size: 35
5500 AGTTTTCAGA
5510 GATCAGAGTTGATCTCATTCCAAGAAGTTTCCAAC
1 GATCAGAGTTGATCTCATTCCAAGAAGTTTCCAAC
5545 GATCAGAGTTGATCTCATTCCAAGAAGTTTCCAAC
1 GATCAGAGTTGATCTCATTCCAAGAAGTTTCCAAC
* *
5580 GATCAGAGTTGGTCTCATTCCAAGAGGTTTCCAAC
1 GATCAGAGTTGATCTCATTCCAAGAAGTTTCCAAC
* * *
5615 AATCAGAGTTGATCTCATCCCAAGAAGTTTTCGAA-
1 GATCAGAGTTGATCTCATTCCAAGAAG-TTTCCAAC
*
5650 GATCAGAGTTGATCTCATTCCAAGAAGTTTTCGAA-
1 GATCAGAGTTGATCTCATTCCAAGAAG-TTTCCAAC
* * * *
5685 GATCAGAGTTGATCTCATTCCAATAAGTTTTCGAT
1 GATCAGAGTTGATCTCATTCCAAGAAGTTTCCAAC
* *
5720 GATCAGAGTTTATCTCATTCCAAGAAGTTTTCAAC
1 GATCAGAGTTGATCTCATTCCAAGAAGTTTCCAAC
* * *
5755 GATCAGAGTTGATCTCATTTCAAGAAGTTTTCAAT
1 GATCAGAGTTGATCTCATTCCAAGAAGTTTCCAAC
*
5790 GATCAGAATTGATCTCA
1 GATCAGAGTTGATCTCA
5807 GATTGATCCG
Statistics
Matches: 239, Mismatches: 21, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
34 4 0.02
35 229 0.96
36 6 0.03
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Consensus pattern (35 bp):
GATCAGAGTTGATCTCATTCCAAGAAGTTTCCAAC
Found at i:5936 original size:54 final size:54
Alignment explanation
Indices: 5769--5936 Score: 223
Period size: 54 Copynumber: 3.1 Consensus size: 54
5759 AGAGTTGATC
* * * *
5769 TCATTTCAAGAAGTTTTC-AATGATCAGAATTGATCT-CAGATTGATCCGGTGCGG
1 TCATTCCAAGAAGTTTTCGGA-GTTCAGAGTTGATCTCCA-ATTGATCCGGTGCGG
* * *
5823 TCATTTCAAGAAGTTTTCGGAGTTCAGAGTTGATCTCGAATTGATCCGATGCGG
1 TCATTCCAAGAAGTTTTCGGAGTTCAGAGTTGATCTCCAATTGATCCGGTGCGG
* *
5877 TCATTCCAAGAAGTTTTTGGAGTTCAGAGTTGATCTCCAATTGACCCGGTGCGG
1 TCATTCCAAGAAGTTTTCGGAGTTCAGAGTTGATCTCCAATTGATCCGGTGCGG
5931 TCATTC
1 TCATTC
5937 TAGAAGGATT
Statistics
Matches: 102, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
54 100 0.98
55 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (54 bp):
TCATTCCAAGAAGTTTTCGGAGTTCAGAGTTGATCTCCAATTGATCCGGTGCGG
Found at i:10100 original size:18 final size:18
Alignment explanation
Indices: 10079--10138 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
10069 ATCTGAAAGA
10079 GCATTAACAGTCATATTT
1 GCATTAACAGTCATATTT
* * ***
10097 GCATT-ACAATCTAAAACA
1 GCATTAACAGTC-ATATTT
*
10115 ACATTAACAGTCATATTT
1 GCATTAACAGTCATATTT
10133 GCATTA
1 GCATTA
10139 CAATCTGAAA
Statistics
Matches: 28, Mismatches: 12, Indels: 4
0.64 0.27 0.09
Matches are distributed among these distances:
17 5 0.18
18 18 0.64
19 5 0.18
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.33
Consensus pattern (18 bp):
GCATTAACAGTCATATTT
Found at i:10101 original size:36 final size:36
Alignment explanation
Indices: 10060--10174 Score: 194
Period size: 36 Copynumber: 3.2 Consensus size: 36
10050 TAGAAACATC
* * *
10060 TGCATTATAATCTGAAAGAGCATTAACAGTCATATT
1 TGCATTACAATCTGAAACAACATTAACAGTCATATT
*
10096 TGCATTACAATCTAAAACAACATTAACAGTCATATT
1 TGCATTACAATCTGAAACAACATTAACAGTCATATT
10132 TGCATTACAATCTGAAACAACATTAACAGTCATATT
1 TGCATTACAATCTGAAACAACATTAACAGTCATATT
10168 TGCATTA
1 TGCATTA
10175 TTACAAGTAG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 74 1.00
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (36 bp):
TGCATTACAATCTGAAACAACATTAACAGTCATATT
Found at i:10251 original size:27 final size:27
Alignment explanation
Indices: 10216--10267 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
10206 GAGAATCAAT
* *
10216 AACAAGATCATGAGAAGTAACATCAGC
1 AACAAGATCATCAGAAGCAACATCAGC
*
10243 AACATGATCATCAGAAGCAACATCA
1 AACAAGATCATCAGAAGCAACATCA
10268 AGCTGGTGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.48, C:0.21, G:0.15, T:0.15
Consensus pattern (27 bp):
AACAAGATCATCAGAAGCAACATCAGC
Found at i:28464 original size:30 final size:30
Alignment explanation
Indices: 28428--28487 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
28418 GGCATCTTTA
* *
28428 TGGCATCTCCATGAGGCTTTGTGATTCCAT
1 TGGCATCTCCATGAGACTTTGCGATTCCAT
28458 TGGCATCTCCATGAGACTTTGCGATTCCAT
1 TGGCATCTCCATGAGACTTTGCGATTCCAT
28488 CCTCTCCTTT
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:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (30 bp):
TGGCATCTCCATGAGACTTTGCGATTCCAT
Found at i:30100 original size:32 final size:32
Alignment explanation
Indices: 30059--30184 Score: 159
Period size: 32 Copynumber: 3.9 Consensus size: 32
30049 ATAGGGGCGT
30059 TAGGGGCGTTCT-ACGAACAAAACGCCACTATA
1 TAGGGGCGTT-TAACGAACAAAACGCCACTATA
* * *
30091 TAGGGGCGTTTTACAAACAAAATGCCACTATA
1 TAGGGGCGTTTAACGAACAAAACGCCACTATA
*
30123 TAGGGGCATTTCAA-GAACAAAACGCCACTATA
1 TAGGGGCGTTT-AACGAACAAAACGCCACTATA
*
30155 T-GGTGGCGTTTAATGAACAAAACGCCACTA
1 TAGG-GGCGTTTAACGAACAAAACGCCACTA
30185 AACGCTCCGA
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
31 5 0.06
32 77 0.93
33 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (32 bp):
TAGGGGCGTTTAACGAACAAAACGCCACTATA
Found at i:34248 original size:24 final size:24
Alignment explanation
Indices: 34195--34248 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
34185 TGGACAACCT
*
34195 ATTGGATTTTATTTAGTGGTTGAC
1 ATTGGCTTTTATTTAGTGGTTGAC
*
34219 ATTGGCTTTTATTTAGTTGTTGAC
1 ATTGGCTTTTATTTAGTGGTTGAC
34243 ATTGGC
1 ATTGGC
34249 ATATAAAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.19, C:0.07, G:0.24, T:0.50
Consensus pattern (24 bp):
ATTGGCTTTTATTTAGTGGTTGAC
Found at i:35110 original size:426 final size:424
Alignment explanation
Indices: 34319--35165 Score: 1487
Period size: 426 Copynumber: 2.0 Consensus size: 424
34309 ATATTATTTG
* *
34319 CTATGTATGATTTCTGTTATGTTGAATCATGGAATTATGTGTGTTTATGGATTGATAAAATTTAT
1 CTATGTATGATTGCTGTTATGTGGAATCATGGAATTATGTGTGTTTATGGATTGATAAAATTTAT
*
34384 GCATGTATTTGTTTAGGTTTGTGATAGAAATGGGTGGAAAGTAATGTTGTTTTCGAAGGTCGTAG
66 GCATGTATTTGTTTAGGTTTGTGATAGAAATGGGTGGAAAGTAATGTTCTTTTCGAAGGTCGTAG
* * * * *
34449 GCCGGATTTATGGAAGTTGGTAGGAAGCAAAGGTCCAAATTAGTGGTTATTGAGGTTGCCACCAT
131 GCCAGATTTATGGAAATTGGGAGGAAGCAAAGGTCCAAATTAATGGTTATCGAGGTTGCCACCAT
*
34514 AAGATGTACAAGGATCAAAAGGAAGCGGAAATGACTTTTCTTGAGTATTGGAACCTCAATGAGGT
196 AAGATGTACAAGGATCAAAAGGAAGCGGAAATGACTTTTCTCGAGTATTGGAACCTCAATGAGGT
*
34579 TGATGAGAAAGTAATTAAGAAACAATCCTTGAAAATGAAAGAGATGAAAGCTTCTATTATTGATC
261 TGATGAGAAAGTAATTAAGAAACAACCCTTGAAAATGAAAGAGATGAAAGCTTCTATTATTGATC
**
34644 AATAATTTCATAAAGGATTAATTCTGCGATTTGTGGTAGGGGTTACCACATTGTTTATTTTGTGG
326 AATAATTTCATAAAGGATTAATTCTGCGATTTGTGGTAGGGGTTACCACATTGTTTATTTTGTAA
*
34709 GTTGGAAAATGAATTAGATTAGTGTAGTAAGCTT
391 GTTAGAAAATGAATTAGATTAGTGTAGTAAGCTT
*
34743 CTATGTATGATTGCTGTTATGTGGAATCATGGAATTTTGTGTGTTTATGGATTGATAAAATTTAT
1 CTATGTATGATTGCTGTTATGTGGAATCATGGAATTATGTGTGTTTATGGATTGATAAAATTTAT
*
34808 GCATTTATTTGTTTAGGTTTGTGATAGAAATGGGTGGAAAGTATTATGTTCTTTTCGAAGGTCGT
66 GCATGTATTTGTTTAGGTTTGTGATAGAAATGGGTGGAAAGTA--ATGTTCTTTTCGAAGGTCGT
*
34873 AGGCCAGATTTATGGAAATTGGGAGGAAGCAAAGGTCCAAATTAATGGTTATCGAGGTTGCTACC
129 AGGCCAGATTTATGGAAATTGGGAGGAAGCAAAGGTCCAAATTAATGGTTATCGAGGTTGCCACC
*
34938 ATAAGATGTACAAGGATCAAAATGAAGCGGAAATGACTTTTCTCGAGTATTGGAACCTCAATGAG
194 ATAAGATGTACAAGGATCAAAAGGAAGCGGAAATGACTTTTCTCGAGTATTGGAACCTCAATGAG
*
35003 GTTGATGAGAAAGTAATTAAGAAACAACCCTTGAAAATGAAAGAGATGAAAGTTTCTATTATTGA
259 GTTGATGAGAAAGTAATTAAGAAACAACCCTTGAAAATGAAAGAGATGAAAGCTTCTATTATTGA
** *
35068 TCAATGCTTTCATAAAGGATTAATTGTGCGATTTGTGGTAGGGGTTACCACATTGTTTATTTTGT
324 TCAATAATTTCATAAAGGATTAATTCTGCGATTTGTGGTAGGGGTTACCACATTGTTTATTTTGT
35133 AAGTTAGAAAATGAATTAGATTAGTGTAGTAAG
389 AAGTTAGAAAATGAATTAGATTAGTGTAGTAAG
35166 GCCCAAATTA
Statistics
Matches: 400, Mismatches: 21, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
424 104 0.26
426 296 0.74
ACGTcount: A:0.32, C:0.09, G:0.25, T:0.35
Consensus pattern (424 bp):
CTATGTATGATTGCTGTTATGTGGAATCATGGAATTATGTGTGTTTATGGATTGATAAAATTTAT
GCATGTATTTGTTTAGGTTTGTGATAGAAATGGGTGGAAAGTAATGTTCTTTTCGAAGGTCGTAG
GCCAGATTTATGGAAATTGGGAGGAAGCAAAGGTCCAAATTAATGGTTATCGAGGTTGCCACCAT
AAGATGTACAAGGATCAAAAGGAAGCGGAAATGACTTTTCTCGAGTATTGGAACCTCAATGAGGT
TGATGAGAAAGTAATTAAGAAACAACCCTTGAAAATGAAAGAGATGAAAGCTTCTATTATTGATC
AATAATTTCATAAAGGATTAATTCTGCGATTTGTGGTAGGGGTTACCACATTGTTTATTTTGTAA
GTTAGAAAATGAATTAGATTAGTGTAGTAAGCTT
Found at i:40644 original size:2 final size:2
Alignment explanation
Indices: 40639--40673 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
40629 AAAAGGAAAA
40639 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
40674 AATTGAGAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Done.