Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013222.1 Corchorus capsularis cultivar CVL-1 contig13243, 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: 23951
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:4625 original size:24 final size:25
Alignment explanation
Indices: 4565--4623 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
4555 TTCAAACCCT
*
4565 AAACTTCATTTCTAACAACTTCTTC
1 AAACTTCATTTCTAACAACATCTTC
4590 AAACTTCATTTCTAACAA-ATCTTC
1 AAACTTCATTTCTAACAACATCTTC
4614 AAA-TTCATTT
1 AAACTTCATTT
4624 TCCTTCATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 7 0.21
24 8 0.24
25 18 0.55
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.41
Consensus pattern (25 bp):
AAACTTCATTTCTAACAACATCTTC
Found at i:4662 original size:26 final size:26
Alignment explanation
Indices: 4633--4700 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
4623 TTCCTTCATT
4633 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
4659 TTAATCATAAACTAATTAAATATTAA
1 TTAATCATAAACTAATTAAATACTAA
*
4685 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
4701 AAACTAAGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.35
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:4663 original size:15 final size:15
Alignment explanation
Indices: 4633--4677 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
4623 TTCCTTCATT
4633 TTAATCATAAACTAA
1 TTAATCATAAACTAA
4648 TTAA--AT--ACTAA
1 TTAATCATAAACTAA
4659 TTAATCATAAACTAA
1 TTAATCATAAACTAA
4674 TTAA
1 TTAA
4678 ATATTAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
11 9 0.35
13 4 0.15
15 13 0.50
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (15 bp):
TTAATCATAAACTAA
Found at i:6372 original size:441 final size:438
Alignment explanation
Indices: 5288--6380 Score: 1454
Period size: 441 Copynumber: 2.5 Consensus size: 438
5278 AAACAAATCA
* * *
5288 TTTTTGCCGGTTTATTTATTAAATGATCCATATACTTTTATGCTTTATGTTATTTAGTCCCTCAC
1 TTTTTGCTGGATTATTTATCAAATGATCCATATACTTTTATGCTTTATGTTATTTAGTCCCTCAC
* * * * * * *
5353 AATTTTTGGGTTGGACGATTGAACGTTTCGAC-TTTAATTATTATTTTTTTTTTGTTTGTCCGAT
66 AAATTATGGGTTGGACGATTGAACGTTT-GACTTTTATTTTTTATTTTTGTTTTATTTGTCTGAT
* *
5417 AAAGGTGATTCAAGTGTCTATTAAAAAGTAATTTCATGATCTACAACTTCCATGAAGGACTCAAA
130 AAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAGGACTCAAA
* * * *
5482 AGCCCATTTTAATGTTTTGATTCAAAAAAATGCTTCTGAAATTTTATGGTCTCGATTGTTGGTCT
195 AGCCAATTTTAATGTTTTGACTCAAAAAAATGCTTCTGAAATTTTATGGTCTCCATTGTCGGTCT
* * ** *
5547 ATTTGATATCGTATAAATTTCGGTCCACTTGTCCGATTGAGGTTGTTCAAGTGTCGGTTAAAAGG
260 ATTTAATATCATATAAATTTCAATCCACTTGTCCGATTGAGGTTGTTCAAGTGTCGATTAAAAGG
* ** * *
5612 TTATTGTGTAATCTATGACTTTCGTTAAGGGCCTGAAAGCTGAATTTGATTGATGAGTTTCGTGG
325 TTATTGTATAATCTACAACTTTCGTTAAGGGCCTGAAAGCTGAATTTGATTAATGAGTTTCGTAG
*
5677 AGGGTTCAAGAGGGAATTTTTATGTTTGGTCTCCATAAACAAAAAAAAT
390 AAGGTTCAAGAGGGAATTTTTATGTTTGGTCTCCATAAACAAAAAAAAT
* * **
5726 TTTTTGCTGTATTATTTATCAAATGATCCCTATACTTTTATAATTTATGTTATTTAGTCCCTCAC
1 TTTTTGCTGGATTATTTATCAAATGATCCATATACTTTTATGCTTTATGTTATTTAGTCCCTCAC
* * * *
5791 AAATTCTGGGTTGGACGATTGAACGTTTCAGCTTTAATTCTTTTATTTTTCGTTTTTTTTGTCTG
66 AAATTATGGGTTGGACGATTGAACGTTTGA-CTTTTATT-TTTTATTTTT-GTTTTATTTGTCTG
* * *
5856 ATGAAGGTGATTCAATTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAGGACCCA
128 ATAAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAGGACTCA
* * *
5921 AAAGCCAATTTTAATGTTTTGACTCTAAAAAATGCTTTTGAAATTTTGTGGTCTCCATTGTCGGT
193 AAAGCCAATTTTAATGTTTTGACTCAAAAAAATGCTTCTGAAATTTTATGGTCTCCATTGTCGGT
* * * * *
5986 CTATTTAATATTATGTAATTTTCAATGCACTTGTCTGATTGAGGTTGTTCAAGTGTCGATTAAAA
258 CTATTTAATATCATATAAATTTCAATCCACTTGTCCGATTGAGGTTGTTCAAGTGTCGATTAAAA
* *
6051 GGTTATTGTATGATCTACAACTTTCGTTAAGGGCTTGAAAGCTGAATTTGATTAATGAGTTTCGT
323 GGTTATTGTATAATCTACAACTTTCGTTAAGGGCCTGAAAGCTGAATTTGATTAATGAGTTTCGT
* * ***
6116 AGAAGGTTCGAGAGGGAATTTTTATGTTTGGTCTCCATAAACAAATATTTT
388 AGAAGGTTCAAGAGGGAATTTTTATGTTTGGTCTCCATAAACAAAAAAAAT
* * * * *
6167 TTTTTGCTGGATTATTTATCAAATGATCCTTATACTTTTTATGCTTTATGCTATTTAATCCTTTA
1 TTTTTGCTGGATTATTTATCAAATGATCCATATAC-TTTTATGCTTTATGTTATTTAGTCCCTCA
* * *
6232 -AAATTATGGGCTGGACGATTTAACGCTTTGACTTTTATTTTTGTATTTTCTGTTCTATTTGTCT
65 CAAATTATGGGTTGGACGATTGAACG-TTTGACTTTTATTTTT-TATTTT-TGTTTTATTTGTCT
* * * * * * * *
6296 GATTAAGATGATTCAAGTGTCTATGAAAAGGTGATTTCATGATCTATAAATTTCATGAAGAATTC
127 GATAAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAGGACTC
*
6361 AGAAA-CCAATTTTTATGTTT
192 A-AAAGCCAATTTTAATGTTT
6381 CAATTGAAAA
Statistics
Matches: 569, Mismatches: 77, Indels: 15
0.86 0.12 0.02
Matches are distributed among these distances:
437 1 0.00
438 85 0.15
439 4 0.01
440 12 0.02
441 436 0.77
442 31 0.05
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (438 bp):
TTTTTGCTGGATTATTTATCAAATGATCCATATACTTTTATGCTTTATGTTATTTAGTCCCTCAC
AAATTATGGGTTGGACGATTGAACGTTTGACTTTTATTTTTTATTTTTGTTTTATTTGTCTGATA
AAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAGGACTCAAAA
GCCAATTTTAATGTTTTGACTCAAAAAAATGCTTCTGAAATTTTATGGTCTCCATTGTCGGTCTA
TTTAATATCATATAAATTTCAATCCACTTGTCCGATTGAGGTTGTTCAAGTGTCGATTAAAAGGT
TATTGTATAATCTACAACTTTCGTTAAGGGCCTGAAAGCTGAATTTGATTAATGAGTTTCGTAGA
AGGTTCAAGAGGGAATTTTTATGTTTGGTCTCCATAAACAAAAAAAAT
Found at i:7042 original size:16 final size:17
Alignment explanation
Indices: 7016--7048 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
7006 AAACGCTAGT
7016 AAACTACGTTTCCTCTC
1 AAACTACGTTTCCTCTC
*
7033 AAAC-ACGTTTTCTCTC
1 AAACTACGTTTCCTCTC
7049 TGTAACCAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.24, C:0.33, G:0.06, T:0.36
Consensus pattern (17 bp):
AAACTACGTTTCCTCTC
Found at i:16645 original size:40 final size:40
Alignment explanation
Indices: 16601--16680 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
16591 CCACTCCAAC
*
16601 TTCCTGCTGTAAAAGTCGACGCTCTTTTCAATAAATGGGT
1 TTCCTGCTGTAAAAGTCGACGCTCTTCTCAATAAATGGGT
* *
16641 TTCCTGCTGTAGAAGTCGACGCTCTTCTCAATCAATGGGT
1 TTCCTGCTGTAAAAGTCGACGCTCTTCTCAATAAATGGGT
16681 GGCAGAGAGC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.34
Consensus pattern (40 bp):
TTCCTGCTGTAAAAGTCGACGCTCTTCTCAATAAATGGGT
Found at i:17571 original size:58 final size:58
Alignment explanation
Indices: 17501--17613 Score: 226
Period size: 58 Copynumber: 1.9 Consensus size: 58
17491 TATTCTCTTC
17501 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
1 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
17559 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATA
1 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATA
17614 TCAAAGTCCC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.42, C:0.26, G:0.14, T:0.19
Consensus pattern (58 bp):
AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
Found at i:17608 original size:26 final size:26
Alignment explanation
Indices: 17498--17601 Score: 88
Period size: 26 Copynumber: 3.8 Consensus size: 26
17488 TAATATTCTC
17498 TTCAAAAGTCCTCAAACACAAGGGCA
1 TTCAAAAGTCCTCAAACACAAGGGCA
*
17524 TTCATAAGTCC-CTAAACAC-AGAGGCA
1 TTCAAAAGTCCTC-AAACACAAG-GGCA
17550 TCTATACTAAAAAGTCCTCAAACACAAGGGCA
1 --T-T-C--AAAAGTCCTCAAACACAAGGGCA
*
17582 TTCATAAGTCC-CTAAACACA
1 TTCAAAAGTCCTC-AAACACA
17602 GAGGCATCTA
Statistics
Matches: 64, Mismatches: 3, Indels: 22
0.72 0.03 0.25
Matches are distributed among these distances:
25 4 0.06
26 34 0.53
28 2 0.03
29 2 0.03
30 2 0.03
32 17 0.27
33 3 0.05
ACGTcount: A:0.41, C:0.27, G:0.12, T:0.19
Consensus pattern (26 bp):
TTCAAAAGTCCTCAAACACAAGGGCA
Found at i:18457 original size:43 final size:43
Alignment explanation
Indices: 18396--18499 Score: 199
Period size: 43 Copynumber: 2.4 Consensus size: 43
18386 CTCATTCCTC
18396 ATTCAACACTTGGGGGCTATGTCAATACAACATATTTCATCAG
1 ATTCAACACTTGGGGGCTATGTCAATACAACATATTTCATCAG
18439 ATTCAACACTTGGGGGCTATGTCAATACAACATATTTCATCAG
1 ATTCAACACTTGGGGGCTATGTCAATACAACATATTTCATCAG
*
18482 ATTCAGCACTTGGGGGCT
1 ATTCAACACTTGGGGGCT
18500 GCAGAAACCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (43 bp):
ATTCAACACTTGGGGGCTATGTCAATACAACATATTTCATCAG
Found at i:18530 original size:35 final size:35
Alignment explanation
Indices: 18482--18569 Score: 95
Period size: 35 Copynumber: 2.5 Consensus size: 35
18472 ATTTCATCAG
* * *
18482 ATTCAGCACTTGGGGGCTGCAGAAACCCCTTCATC
1 ATTCAACACTTGGGGGCTCCAGAAACCCATTCATC
* ** * *
18517 ATTCAACAGTTGGGTACTCCAGAAACTCATTCTTC
1 ATTCAACACTTGGGGGCTCCAGAAACCCATTCATC
*
18552 ATTCAATACTTGGGGGCT
1 ATTCAACACTTGGGGGCT
18570 TCAACAACGA
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.28
Consensus pattern (35 bp):
ATTCAACACTTGGGGGCTCCAGAAACCCATTCATC
Found at i:19016 original size:72 final size:72
Alignment explanation
Indices: 18925--19344 Score: 533
Period size: 72 Copynumber: 5.8 Consensus size: 72
18915 CACATGGTCC
* * * * *
18925 TCTTCTTCATTGTGATTGTAGCTGAGGCAGTTCCCACATTTGGCAGTCATTCCCACAATCCTTAC
1 TCTTCATCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC
* *
18990 ATGATAA
66 GTGATTA
* * *
18997 TCTTCCAT-ATTTCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCTA-TCCTTCACACAATCCTT
1 TCTT-CATCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGC-AGTCCTTCGCACAATCCTT
* *
19060 ACATGATAA
64 ACGTGATTA
* *
19069 TCTTCCAT-ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAACCCTTA
1 TCTT-CATCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTA
* *
19133 TGCGATTA
65 CGTGATTA
* * * *
19141 TATTCATCATTGCGATTGTAGCCGATGCAGTTCCCACATTTGGCAGTCCTTCGCACAACCCTTAT
1 TCTTCATCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC
*
19206 GCGATTA
66 GTGATTA
* * *
19213 TATTCATCATTGCGATTGTAGCCGAGACAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAG
1 TCTTCATCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC
19278 GTGATTA
66 GTGATTA
* * * *
19285 TCTTCTTCATTGCGATTGTAGCCAAGGCAATTCCCACA-TAGGCAGTCCTTCGCACAATCC
1 TCTTCATCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCC
19345 ATGCTACTAC
Statistics
Matches: 316, Mismatches: 28, Indels: 9
0.90 0.08 0.03
Matches are distributed among these distances:
71 25 0.08
72 288 0.91
73 3 0.01
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.32
Consensus pattern (72 bp):
TCTTCATCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC
GTGATTA
Found at i:22912 original size:21 final size:21
Alignment explanation
Indices: 22873--22921 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
22863 TCAATGCTTT
**
22873 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
22895 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
22916 A-GAAGC
1 AGGAAGC
22922 TACAATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCAA
Done.