Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013562.1 Corchorus capsularis cultivar CVL-1 contig13583, 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: 15067
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Found at i:2715 original size:13 final size:14
Alignment explanation
Indices: 2690--2724 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
2680 ACACAAAATG
2690 ATCATTCTGATTA-A
1 ATCATT-TGATTACA
2704 ATCATTTGATTACA
1 ATCATTTGATTACA
2718 ATCATTT
1 ATCATTT
2725 TGTTTAACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.34, C:0.14, G:0.06, T:0.46
Consensus pattern (14 bp):
ATCATTTGATTACA
Found at i:5504 original size:26 final size:26
Alignment explanation
Indices: 5454--5506 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
5444 CAAAAGCTGA
5454 CCCGAACCCGATTAACCGCCCAACCCG
1 CCCGAACCCGA-TAACCGCCCAACCCG
5481 CCCGAACCCG-TAACCCGCCCAACCCG
1 CCCGAACCCGATAA-CCGCCCAACCCG
5507 ATTTGACTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 3 0.12
26 12 0.48
27 10 0.40
ACGTcount: A:0.25, C:0.55, G:0.15, T:0.06
Consensus pattern (26 bp):
CCCGAACCCGATAACCGCCCAACCCG
Found at i:5506 original size:16 final size:17
Alignment explanation
Indices: 5475--5506 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5465 TTAACCGCCC
5475 AACCCGCCCGAACCCGT
1 AACCCGCCCGAACCCGT
5492 AACCCGCCC-AACCCG
1 AACCCGCCCGAACCCG
5507 ATTTGACTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.25, C:0.56, G:0.16, T:0.03
Consensus pattern (17 bp):
AACCCGCCCGAACCCGT
Found at i:5593 original size:16 final size:17
Alignment explanation
Indices: 5560--5604 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
5550 AACCCGACTA
*
5560 ACCCGTGACCCG-ATTG
1 ACCCGAGACCCGTATTG
5576 ACCCGAGACCCGTA-TG
1 ACCCGAGACCCGTATTG
*
5592 ACCCGAAACCCGT
1 ACCCGAGACCCGT
5605 GAAACCCGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 25 0.96
17 1 0.04
ACGTcount: A:0.24, C:0.40, G:0.22, T:0.13
Consensus pattern (17 bp):
ACCCGAGACCCGTATTG
Found at i:5801 original size:13 final size:14
Alignment explanation
Indices: 5783--5819 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
5773 AATTTAAATT
5783 ATAGAATAAAG-AA
1 ATAGAATAAAGAAA
*
5796 ATAGAATATAGAAA
1 ATAGAATAAAGAAA
5810 ATAGAATAAA
1 ATAGAATAAA
5820 CTTGTTTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.19
Consensus pattern (14 bp):
ATAGAATAAAGAAA
Found at i:6197 original size:16 final size:15
Alignment explanation
Indices: 6178--6293 Score: 101
Period size: 16 Copynumber: 7.6 Consensus size: 15
6168 CTGACCCATT
6178 TGACCCGAGACCCGAA
1 TGACCCGA-ACCCGAA
** *
6194 TGACCCGAAGTCTAA
1 TGACCCGAACCCGAA
6209 --ACCCGAACCCGAA
1 TGACCCGAACCCGAA
* *
6222 TAACCCGAGACCCGAT
1 TGACCCGA-ACCCGAA
*
6238 TGACCCGAAACCCGAT
1 TGACCCG-AACCCGAA
* *
6254 TAACCCGAACCCAAA
1 TGACCCGAACCCGAA
6269 TGACCCGAAACCCGAA
1 TGACCCG-AACCCGAA
*
6285 TGACTCGAA
1 TGACCCGAA
6294 AAAACTAACT
Statistics
Matches: 81, Mismatches: 14, Indels: 11
0.76 0.13 0.10
Matches are distributed among these distances:
13 10 0.12
15 24 0.30
16 46 0.57
17 1 0.01
ACGTcount: A:0.35, C:0.36, G:0.18, T:0.10
Consensus pattern (15 bp):
TGACCCGAACCCGAA
Found at i:6273 original size:31 final size:32
Alignment explanation
Indices: 6209--6285 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 32
6199 CGAAGTCTAA
* *
6209 ACCCG-AACCCGAATAACCCGAGACCCGATTG
1 ACCCGAAACCCGAATAACCCGAGACCCAAATG
*
6240 ACCCGAAACCCGATTAACCCGA-ACCCAAATG
1 ACCCGAAACCCGAATAACCCGAGACCCAAATG
6271 ACCCGAAACCCGAAT
1 ACCCGAAACCCGAAT
6286 GACTCGAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 26 0.63
32 15 0.37
ACGTcount: A:0.36, C:0.39, G:0.16, T:0.09
Consensus pattern (32 bp):
ACCCGAAACCCGAATAACCCGAGACCCAAATG
Found at i:9122 original size:13 final size:14
Alignment explanation
Indices: 9104--9138 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
9094 CATTAATGAT
*
9104 CAAACACCAAAA-C
1 CAAACAACAAAAGC
9117 CAAACAACAAAAGC
1 CAAACAACAAAAGC
9131 CAAACAAC
1 CAAACAAC
9139 TCTGGTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.63, C:0.34, G:0.03, T:0.00
Consensus pattern (14 bp):
CAAACAACAAAAGC
Found at i:13570 original size:48 final size:48
Alignment explanation
Indices: 13410--13825 Score: 365
Period size: 49 Copynumber: 8.6 Consensus size: 48
13400 AAAAATCAAA
* *
13410 CCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTCACCCGTTATTT
1 CCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTGTT-TTT
*
13459 CCCAAAATGCTCTTCCCGGACGGAAGGCATTTGATTTTACCTGTTATTT
1 CCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTGTT-TTT
* * * * *
13508 CCCAAAATGCCCTTTCCGGATGGAATGTATTTGATTTTACTTGTTTTT
1 CCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTGTTTTT
* * * * *
13556 CCCAAAACGCCCTTTCCGGACGGAAGGCA-CTAATCCTTACCTGTTTTT
1 CCCAAAATGCCCTTCCCGGACGGAAGGCATTTGAT-TTTACCTGTTTTT
* *
13604 CCCAAAATGCCCTTCCCGGACGGAAGGCACTT-ATTTTACTTGCTATTTT
1 CCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTG-T-TTTT
* * * ** * *
13653 CCAAAAATGCCCTTCCCGGATGGAAGACGCTT-ATTTTTACCTACTTTTC
1 CCCAAAATGCCCTTCCCGGACGGAAGGCATTTGA-TTTTACCT-GTTTTT
* * * *
13702 CCCAAAGTGCCCTTCCCGGACGGAAGGCA-CTAATTTTTACTTGTTTTTT
1 CCCAAAATGCCCTTCCCGGACGGAAGGCATTTGA-TTTTACCTG-TTTTT
* * ** * * * *
13751 TCTAAAACACCCTTCCCGGATGGAAGGCGTTAG-TTTTACTCGGTTTTT
1 CCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTAC-CTGTTTTT
** * *
13799 CTTAAAATGCCCTTTCCGGACGAAAGG
1 CCCAAAATGCCCTTCCCGGACGGAAGG
13826 TAAGTTCGCT
Statistics
Matches: 300, Mismatches: 57, Indels: 21
0.79 0.15 0.06
Matches are distributed among these distances:
47 9 0.03
48 101 0.34
49 182 0.61
50 8 0.03
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.33
Consensus pattern (48 bp):
CCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTGTTTTT
Found at i:13738 original size:98 final size:98
Alignment explanation
Indices: 13410--13825 Score: 382
Period size: 97 Copynumber: 4.3 Consensus size: 98
13400 AAAAATCAAA
* * ** * *
13410 CCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTCACCCGTTA-TTTCCCAAAATGCTCTTC
1 CCCAAAATGCCCTTCCCGGACGGAAGGCATCTGATTTTACTTGTTATTTTCCAAAAATGCCCTTC
*
13474 CCGGACGGAAGGCATTTGA-TTTTACCTGTTATTT
66 CCGGACGGAAGGCACTT-ATTTTTACCTGTT-TTT
* * * * * * * *
13508 CCCAAAATGCCCTTTCCGGATGGAATGTATTTGATTTTACTTG-T-TTTTCCCAAAACGCCCTTT
1 CCCAAAATGCCCTTCCCGGACGGAAGGCATCTGATTTTACTTGTTATTTTCCAAAAATGCCCTTC
* **
13571 CCGGACGGAAGGCACTAATCCTTACCTGTTTTT
66 CCGGACGGAAGGCACTTATTTTTACCTGTTTTT
* *
13604 CCCAAAATGCCCTTCCCGGACGGAAGGCA-CTTATTTTACTTGCTATTTTCCAAAAATGCCCTTC
1 CCCAAAATGCCCTTCCCGGACGGAAGGCATCTGATTTTACTTGTTATTTTCCAAAAATGCCCTTC
* * * * *
13668 CCGGATGGAAGACGCTTATTTTTACCTACTTTTC
66 CCGGACGGAAGGCACTTATTTTTACCT-GTTTTT
* * * *
13702 CCCAAAGTGCCCTTCCCGGACGGAAGGCA-CTAATTTTTACTTGTTTTTTTCTAAAACA--CCCT
1 CCCAAAATGCCCTTCCCGGACGGAAGGCATCTGA-TTTTACTTGTTATTTTCCAAAA-ATGCCCT
* * * *
13764 TCCCGGATGGAAGGC-GTTAGTTTTACTCGGTTTTT
64 TCCCGGACGGAAGGCACTTATTTTTAC-CTGTTTTT
** * *
13799 CTTAAAATGCCCTTTCCGGACGAAAGG
1 CCCAAAATGCCCTTCCCGGACGGAAGG
13826 TAAGTTCGCT
Statistics
Matches: 263, Mismatches: 47, Indels: 17
0.80 0.14 0.05
Matches are distributed among these distances:
95 11 0.04
96 30 0.11
97 112 0.43
98 90 0.34
99 19 0.07
100 1 0.00
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.33
Consensus pattern (98 bp):
CCCAAAATGCCCTTCCCGGACGGAAGGCATCTGATTTTACTTGTTATTTTCCAAAAATGCCCTTC
CCGGACGGAAGGCACTTATTTTTACCTGTTTTT
Found at i:13742 original size:194 final size:195
Alignment explanation
Indices: 13410--13778 Score: 442
Period size: 194 Copynumber: 1.9 Consensus size: 195
13400 AAAAATCAAA
* * * *
13410 CCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTCACCCGTTATTTCCCAAAATGCTCTTCC
1 CCCAAAATGCCCTTCCCGGACGGAAGGCACTTGATTTCACCCGCTATTTCCAAAAATGCCCTTCC
* * * * * * * * *
13475 CGGACGGAAGGCATTTGATTTTACCTGTTATTTCCCAAAATGCCCTTTCCGGATGGAATGTATTT
66 CGGACGGAAGACACTTGATTTTACCTCTTATTCCCCAAAATGCCCTTCCCGGACGGAAGGCATCT
* * *
13540 GATTTTACTTG-TTTTTCCCAAAACGCCCTTTCCGGACGGAAGGCACTAATCCTTACCTGTTTTT
131 AATTTTACTTGTTTTTTCCCAAAACACCCTTCCCGGACGGAAGGCACTAATCCTTACCTGTTTTT
* **
13604 CCCAAAATGCCCTTCCCGGACGGAAGGCACTT-ATTTTACTTGCTATTTTCCAAAAATGCCCTTC
1 CCCAAAATGCCCTTCCCGGACGGAAGGCACTTGATTTCACCCGCTA-TTTCCAAAAATGCCCTTC
* * *
13668 CCGGATGGAAGACGCTT-ATTTTTACCTACTT-TTCCCCAAAGTGCCCTTCCCGGACGGAAGGCA
65 CCGGACGGAAGACACTTGA-TTTTACCT-CTTATTCCCCAAAATGCCCTTCCCGGACGGAAGGCA
* * *
13731 -CTAATTTTTACTTGTTTTTTTCTAAAACACCCTTCCCGGATGGAAGGC
128 TCTAA-TTTTACTTGTTTTTTCCCAAAACACCCTTCCCGGACGGAAGGC
13779 GTTAGTTTTA
Statistics
Matches: 145, Mismatches: 25, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
193 12 0.08
194 103 0.71
195 30 0.21
ACGTcount: A:0.23, C:0.28, G:0.17, T:0.32
Consensus pattern (195 bp):
CCCAAAATGCCCTTCCCGGACGGAAGGCACTTGATTTCACCCGCTATTTCCAAAAATGCCCTTCC
CGGACGGAAGACACTTGATTTTACCTCTTATTCCCCAAAATGCCCTTCCCGGACGGAAGGCATCT
AATTTTACTTGTTTTTTCCCAAAACACCCTTCCCGGACGGAAGGCACTAATCCTTACCTGTTTTT
Found at i:14686 original size:1 final size:1
Alignment explanation
Indices: 14675--14728 Score: 90
Period size: 1 Copynumber: 54.0 Consensus size: 1
14665 TGAAGAAGAG
* *
14675 AAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
14729 CCTTTGACAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.96, C:0.00, G:0.02, T:0.02
Consensus pattern (1 bp):
A
Done.