Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010957.1 Corchorus capsularis cultivar CVL-1 contig10978, 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: 34665
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1133 original size:33 final size:32
Alignment explanation
Indices: 1085--1181 Score: 113
Period size: 33 Copynumber: 3.0 Consensus size: 32
1075 CAAGTGACCG
*
1085 GCCACGCGACTTGGAGATGCCCGCGCAACACCA
1 GCCACGCGACATGGAGATGCCCG-GCAACACCA
* * *
1118 GCCATGCGACATGGAGATGCCCGGTCATCACCG
1 GCCACGCGACATGGAGATGCCCGG-CAACACCA
** *
1151 GCCACGCGACATGGCCATGCCCGGCCACACC
1 GCCACGCGACATGGAGATGCCCGGCAACACC
1182 CAGTCACATG
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
32 6 0.11
33 48 0.89
ACGTcount: A:0.22, C:0.40, G:0.28, T:0.10
Consensus pattern (32 bp):
GCCACGCGACATGGAGATGCCCGGCAACACCA
Found at i:1356 original size:90 final size:90
Alignment explanation
Indices: 1195--1372 Score: 322
Period size: 90 Copynumber: 2.0 Consensus size: 90
1185 TCACATGACT
*
1195 CAGCCAAGCCCGGCCACAACCGGCCACATGATCCTTTATCTATGCCGTTGGGTCCAATAACAAGA
1 CAGCCAAGCCCGGCCACAACCGGCCACATGATCCTTTATCTATGCCATTGGGTCCAATAACAAGA
1260 GCTCAGGCTTAAAGGTTTAAGGAAG
66 GCTCAGGCTTAAAGGTTTAAGGAAG
1285 CAGCCAAGCCCGGCCACAACCGGCCACATGATCCTTTATCTATGCCATTGGGTCCAATAACAA-A
1 CAGCCAAGCCCGGCCACAACCGGCCACATGATCCTTTATCTATGCCATTGGGTCCAATAACAAGA
*
1349 GGGTCAGGCTTAAAGGTTTAAGGA
66 -GCTCAGGCTTAAAGGTTTAAGGA
1373 TGCTTTAGTG
Statistics
Matches: 85, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
89 1 0.01
90 84 0.99
ACGTcount: A:0.29, C:0.28, G:0.23, T:0.20
Consensus pattern (90 bp):
CAGCCAAGCCCGGCCACAACCGGCCACATGATCCTTTATCTATGCCATTGGGTCCAATAACAAGA
GCTCAGGCTTAAAGGTTTAAGGAAG
Found at i:1424 original size:10 final size:10
Alignment explanation
Indices: 1409--1461 Score: 56
Period size: 10 Copynumber: 5.2 Consensus size: 10
1399 ATCTTGAAGA
1409 ATTGAAGACC
1 ATTGAAGACC
1419 ATTGAAGACTC
1 ATTGAAGAC-C
*
1430 ATTG--GGCC
1 ATTGAAGACC
1438 GATTTGAAGACC
1 -A-TTGAAGACC
1450 ATTGAAGACC
1 ATTGAAGACC
1460 AT
1 AT
1462 GTTGTGTACA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
8 1 0.03
9 3 0.08
10 23 0.64
11 6 0.17
12 3 0.08
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.25
Consensus pattern (10 bp):
ATTGAAGACC
Found at i:4027 original size:2 final size:2
Alignment explanation
Indices: 4022--4048 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4012 TCTAAAAAAC
4022 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4049 CAAGTATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4585 original size:18 final size:17
Alignment explanation
Indices: 4555--4600 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
4545 TTGAATTCAA
4555 TATTTTTAAAATTATTT
1 TATTTTTAAAATTATTT
* *
4572 TATTTTTACCAATTTTTT
1 TATTTTTA-AAATTATTT
*
4590 TTTTTTTAAAA
1 TATTTTTAAAA
4601 ATAGAGACTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTTTTAAAATTATTT
Found at i:4801 original size:17 final size:16
Alignment explanation
Indices: 4779--4812 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4769 TTGTTTGGCA
*
4779 TCGTTTTTGTTTTTGTT
1 TCGTTTTCG-TTTTGTT
4796 TCGTTTTCGTTTTGTT
1 TCGTTTTCGTTTTGTT
4812 T
1 T
4813 TTGTTACACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.00, C:0.09, G:0.18, T:0.74
Consensus pattern (16 bp):
TCGTTTTCGTTTTGTT
Found at i:5686 original size:43 final size:47
Alignment explanation
Indices: 5622--5710 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 47
5612 AAATTCAATA
*
5622 TTTTTATAAATATTTTATTTTACCATTTTAATTTT-AATAAATTGGC
1 TTTTTATAAATATTTTATTTTACCATTTTAATTTTAAAAAAATTGGC
* *
5668 TTTTT-TAAATA-TTT-TTTTACGATTTTATTTTTAAAAAAATTGG
1 TTTTTATAAATATTTTATTTTACCATTTTAATTTTAAAAAAATTGG
5711 AGATTTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
43 16 0.41
44 12 0.31
45 6 0.15
46 5 0.13
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.57
Consensus pattern (47 bp):
TTTTTATAAATATTTTATTTTACCATTTTAATTTTAAAAAAATTGGC
Found at i:7080 original size:42 final size:42
Alignment explanation
Indices: 7033--7137 Score: 138
Period size: 42 Copynumber: 2.5 Consensus size: 42
7023 TTTTTAATGT
*
7033 TCTAACATTTTCAAGCGTTATAGATTGCACTGGTTAGCTGAA
1 TCTAACATTTTCAAGCGTTACAGATTGCACTGGTTAGCTGAA
* * * * * *
7075 TCTAACATTTTCAAGCATTACATATTGTATTGGTTGGCTGAT
1 TCTAACATTTTCAAGCGTTACAGATTGCACTGGTTAGCTGAA
*
7117 TCTAACATTTTCAGGCGTTAC
1 TCTAACATTTTCAAGCGTTAC
7138 GTACAGATTG
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (42 bp):
TCTAACATTTTCAAGCGTTACAGATTGCACTGGTTAGCTGAA
Found at i:7470 original size:42 final size:42
Alignment explanation
Indices: 7411--7551 Score: 149
Period size: 42 Copynumber: 3.4 Consensus size: 42
7401 CTTTTCTAAT
*
7411 ATTCTAACATTTTCATGCATTGCAGATTGCATTGGCTGGCTG
1 ATTCTAACATTTTCATGCATTGCAGATTGCACTGGCTGGCTG
* * * *
7453 ATTCTAACATTTTCATGCGTTGTAGATTGTACTGGTTGGCTG
1 ATTCTAACATTTTCATGCATTGCAGATTGCACTGGCTGGCTG
* * * * * * *
7495 ATTCTAACATTTTTAGGCGTTACAGATT-CTACTAGTTGGTTG
1 ATTCTAACATTTTCATGCATTGCAGATTGC-ACTGGCTGGCTG
*
7537 ATTATAACATTTTCA
1 ATTCTAACATTTTCA
7552 AGCGTCACAG
Statistics
Matches: 84, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
42 84 1.00
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (42 bp):
ATTCTAACATTTTCATGCATTGCAGATTGCACTGGCTGGCTG
Found at i:7536 original size:46 final size:43
Alignment explanation
Indices: 7411--7682 Score: 142
Period size: 42 Copynumber: 6.7 Consensus size: 43
7401 CTTTTCTAAT
* * * *
7411 ATTCTAACATTTTCATGCATTGCAGATTGC-A-TTGGCTGGCTG
1 ATTCTAACATTTTCAGGCGTTACAGATT-CTACTTGGTTGGCTG
* ** *
7453 ATTCTAACATTTTCATGCGTTGTAGATTGTAC-TGGTTGGCTG
1 ATTCTAACATTTTCAGGCGTTACAGATTCTACTTGGTTGGCTG
* * *
7495 ATTCTAACATTTTTAGGCGTTACAGATTCTAC-TAGTTGGTTG
1 ATTCTAACATTTTCAGGCGTTACAGATTCTACTTGGTTGGCTG
* * * * * *
7537 ATTATAACATTTTCAAGCGTCACAG-GT-T-GTT--CTGGCT-
1 ATTCTAACATTTTCAGGCGTTACAGATTCTACTTGGTTGGCTG
* * * * * *
7574 A-GCT--GATTTTCATGCGTTACAGATTGTAGTT-ATTGGCTG
1 ATTCTAACATTTTCAGGCGTTACAGATTCTACTTGGTTGGCTG
* * * * ** **
7613 ATTCTTACATTTTCAGGCGTAATAGATTGTAC-CAGTTGATTG
1 ATTCTAACATTTTCAGGCGTTACAGATTCTACTTGGTTGGCTG
*
7655 ATTCAAACATTTTCAGGCGTTACAGATT
1 ATTCTAACATTTTCAGGCGTTACAGATT
7683 ATCGAAACGT
Statistics
Matches: 178, Mismatches: 40, Indels: 24
0.74 0.17 0.10
Matches are distributed among these distances:
34 15 0.08
35 1 0.01
36 2 0.01
37 4 0.02
38 9 0.05
39 1 0.01
40 4 0.02
41 1 0.01
42 141 0.79
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.40
Consensus pattern (43 bp):
ATTCTAACATTTTCAGGCGTTACAGATTCTACTTGGTTGGCTG
Found at i:7669 original size:118 final size:118
Alignment explanation
Indices: 7461--7679 Score: 296
Period size: 118 Copynumber: 1.9 Consensus size: 118
7451 TGATTCTAAC
** * * *
7461 ATTTTCATGCGTTGTAGATTGTACTGGTTGGCTGATTCTAACATTTTTAGGCGTTACAGATTCTA
1 ATTTTCATGCGTTACAGATTGTACTGATTGGCTGATTCTAACATTTTCAGGCGTAACAGATTCTA
* *
7526 CTAGTTGGTTGATTATAACATTTTCAAGCGTCACAGGTTGTTCTGGCTAGCTG
66 CCAGTTGATTGATTATAACATTTTCAAGCGTCACAGGTTGTTCTGGCTAGCTG
* * * * *
7579 ATTTTCATGCGTTACAGATTGTAGTTATTGGCTGATTCTTACATTTTCAGGCGTAATAGATTGTA
1 ATTTTCATGCGTTACAGATTGTACTGATTGGCTGATTCTAACATTTTCAGGCGTAACAGATTCTA
* *
7644 CCAGTTGATTGATTCA-AACATTTTCAGGCGTTACAG
66 CCAGTTGATTGATT-ATAACATTTTCAAGCGTCACAG
7680 ATTATCGAAA
Statistics
Matches: 86, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
118 85 0.99
119 1 0.01
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.40
Consensus pattern (118 bp):
ATTTTCATGCGTTACAGATTGTACTGATTGGCTGATTCTAACATTTTCAGGCGTAACAGATTCTA
CCAGTTGATTGATTATAACATTTTCAAGCGTCACAGGTTGTTCTGGCTAGCTG
Found at i:12428 original size:14 final size:14
Alignment explanation
Indices: 12409--12439 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12399 TTAAGAGTAC
*
12409 ACAAAAATGAAGTT
1 ACAAAAATAAAGTT
12423 ACAAAAATAAAGTT
1 ACAAAAATAAAGTT
12437 ACA
1 ACA
12440 TTAAGATGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.10, G:0.10, T:0.19
Consensus pattern (14 bp):
ACAAAAATAAAGTT
Found at i:33360 original size:39 final size:40
Alignment explanation
Indices: 33285--33364 Score: 119
Period size: 39 Copynumber: 2.0 Consensus size: 40
33275 GTGCCCGGGA
33285 AGCCTATTCAACTATTTTCTTCGGCTTCACCCGACCCGAT
1 AGCCTATTCAACTATTTTCTTCGGCTTCACCCGACCCGAT
* *
33325 AGCCTTTTCAACT-TTTT-TTCCGGTTTCACCCGACCCGAT
1 AGCCTATTCAACTATTTTCTT-CGGCTTCACCCGACCCGAT
33364 A
1 A
33365 CCCGAGGTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
38 2 0.05
39 23 0.62
40 12 0.32
ACGTcount: A:0.19, C:0.34, G:0.12, T:0.35
Consensus pattern (40 bp):
AGCCTATTCAACTATTTTCTTCGGCTTCACCCGACCCGAT
Done.