Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012978.1 Corchorus capsularis cultivar CVL-1 contig12999, 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: 31436
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Found at i:1391 original size:2 final size:2
Alignment explanation
Indices: 1384--1431 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
1374 GTAAAAGCAA
1384 AT AT AT AT AT AT AT AT -T AT A- AT -T AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1423 AT AT TT AT A
1 AT AT AT AT A
1432 ATACCCATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
1 3 0.07
2 38 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:4105 original size:14 final size:15
Alignment explanation
Indices: 4072--4107 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
4062 TATTTGTATT
4072 ATATAAAAATATAAAC
1 ATATAAAAATAT-AAC
4088 ATATAAAAATAT-AC
1 ATATAAAAATATAAC
4102 ATATAA
1 ATATAA
4108 TACCAAAGCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.40
16 12 0.60
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (15 bp):
ATATAAAAATATAAC
Found at i:4353 original size:115 final size:114
Alignment explanation
Indices: 4126--4478 Score: 471
Period size: 114 Copynumber: 3.1 Consensus size: 114
4116 CGTCTTTAAC
* * * * **
4126 TTCAGACGCCTCCATTTAGCGGCATCCTGGAC-CAAGGCGCCGTTATATTTTAGCCTTCAGCTTT
1 TTCAGACGCCTCCATTTAGCGGCGT-CTGGGCTCAAGACGCCGCTATATTTTAGCCTTCATTTTT
4190 ACCCAATTTGCCTTCCTCGGAGAAAAATTAAAGATGACGGCGTCTTGAGG
65 ACCCAATTTGCCTTCCTCGGAGAAAAATTAAAGATGACGGCGTCTTGAGG
* *
4240 TTCAGACGCCTCCATTTAGCGGCGTCTGAGGCTC-AGACGCCGCTATTTTTTAGGCTTCAATTTT
1 TTCAGACGCCTCCATTTAGCGGCGTCTG-GGCTCAAGACGCCGCTATATTTTAGCCTTC-ATTTT
* * * * *
4304 TATCCAATTTGTCTTCCTCAGAGAGAAATTAAAGATGGCGGCGTCTTGAGG
64 TACCCAATTTGCCTTCCTCGGAGAAAAATTAAAGATGACGGCGTCTTGAGG
* *
4355 -TCAAGACGCCTCCATTTAACGGCGTCTGGGGTCAAGACGCCGCTATATTTTAGCCTTCATTTTT
1 TTC-AGACGCCTCCATTTAGCGGCGTCTGGGCTCAAGACGCCGCTATATTTTAGCCTTCATTTTT
* * *
4419 ACCCAATTTGCCTTCCGCGGAGAAAAATTAAAGATCACGGCGTTTTGTA-G
65 ACCCAATTTGCCTTCCTCGGAGAAAAATTAAAGATGACGGCGTCTTG-AGG
4469 TTCAGACGCC
1 TTCAGACGCC
4479 GCTATCTTTT
Statistics
Matches: 207, Mismatches: 25, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
113 3 0.01
114 105 0.51
115 99 0.48
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.30
Consensus pattern (114 bp):
TTCAGACGCCTCCATTTAGCGGCGTCTGGGCTCAAGACGCCGCTATATTTTAGCCTTCATTTTTA
CCCAATTTGCCTTCCTCGGAGAAAAATTAAAGATGACGGCGTCTTGAGG
Found at i:4556 original size:82 final size:83
Alignment explanation
Indices: 4389--4560 Score: 249
Period size: 83 Copynumber: 2.1 Consensus size: 83
4379 TCTGGGGTCA
4389 AGACGCCGCTATATTTTAGCCTTCATTTTTACCCAATTTGCCTTCCGCGGAGAAAAATTAAAGAT
1 AGACGCCGCTATATTTTAGCCTTCATTTTTACCCAATTTGCCTTCCGCGGAGAAAAATTAAAGAT
*
4454 CACGGCGTTTTGTAGTTC
66 CACGGCGTCTTGTAGTTC
* * * * *
4472 AGACGCCGCTATCTTTTAGCCTTCTTTTTTACCCAATTTGCGTTCCTCTGAG-AAAATTAAAGAT
1 AGACGCCGCTATATTTTAGCCTTCATTTTTACCCAATTTGCCTTCCGCGGAGAAAAATTAAAGAT
**
4536 GGCGGCGTCTTG-AGGTTC
66 CACGGCGTCTTGTA-GTTC
4554 AGACGCC
1 AGACGCC
4561 TCCATTTAGC
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
81 1 0.01
82 32 0.40
83 47 0.59
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (83 bp):
AGACGCCGCTATATTTTAGCCTTCATTTTTACCCAATTTGCCTTCCGCGGAGAAAAATTAAAGAT
CACGGCGTCTTGTAGTTC
Found at i:6209 original size:33 final size:33
Alignment explanation
Indices: 6167--6229 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
6157 AGCTAAAGGA
*
6167 TCATATGGCCGGTTGTGGCCGGGCATGGCCGAG
1 TCATATGGCCGGGTGTGGCCGGGCATGGCCGAG
*
6200 TCATGTGGCCGGGTGTGGCCGGGCATGGCC
1 TCATATGGCCGGGTGTGGCCGGGCATGGCC
6230 ATATCGCGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.10, C:0.25, G:0.44, T:0.21
Consensus pattern (33 bp):
TCATATGGCCGGGTGTGGCCGGGCATGGCCGAG
Found at i:6241 original size:33 final size:32
Alignment explanation
Indices: 6172--6310 Score: 102
Period size: 33 Copynumber: 4.2 Consensus size: 32
6162 AAGGATCATA
* * * **
6172 TGGCCGGTTGTGGCCGGGCATGGCCGAGTCATG
1 TGGCCGGGTGTGGCCGGGCATCGCC-AATCGCG
*
6205 TGGCCGGGTGTGGCCGGGCATGGCCATATCGCG
1 TGGCCGGGTGTGGCCGGGCATCGCCA-ATCGCG
* * * *
6238 TGGCC-AGTGATGGCCGGGCATCTCCATGTCGCA
1 TGGCCGGGTG-TGGCCGGGCATCGCCA-ATCGCG
* *
6271 TGGCC-GGTGTTGCGCGGGCATCTCCAAGTCGCG
1 TGGCCGGGTGTGGC-CGGGCATCGCCAA-TCGCG
6304 TGGCCGG
1 TGGCCGG
6311 ATCTCTAAGT
Statistics
Matches: 88, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
32 7 0.08
33 80 0.91
34 1 0.01
ACGTcount: A:0.10, C:0.28, G:0.42, T:0.20
Consensus pattern (32 bp):
TGGCCGGGTGTGGCCGGGCATCGCCAATCGCG
Found at i:6320 original size:21 final size:21
Alignment explanation
Indices: 6290--6331 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
6280 TTGCGCGGGC
*
6290 ATCTCCAAGTCGCGTGGCCGG
1 ATCTCCAAGTCGCATGGCCGG
*
6311 ATCTCTAAGTCGCATGGCCGG
1 ATCTCCAAGTCGCATGGCCGG
6332 TCACTTGTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.31, G:0.31, T:0.21
Consensus pattern (21 bp):
ATCTCCAAGTCGCATGGCCGG
Found at i:11684 original size:17 final size:16
Alignment explanation
Indices: 11653--11686 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
11643 GTCGAAATTT
11653 TTTTTTATTTTTTTGA
1 TTTTTTATTTTTTTGA
11669 TTTTTTATATTTTTTGA
1 TTTTTTAT-TTTTTTGA
11686 T
1 T
11687 ATAACTACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (16 bp):
TTTTTTATTTTTTTGA
Found at i:12762 original size:33 final size:31
Alignment explanation
Indices: 12725--12831 Score: 106
Period size: 33 Copynumber: 3.3 Consensus size: 31
12715 GCCGAGTTAT
**
12725 GTGGCCGGGTGTTGCCGGGCATGGCCACATCGC
1 GTGGCC-GGTGTTGCCGGGCATCTCCA-ATCGC
* * *
12758 GTGGCCGGTGATGGCCGGGCATCTCCATGTCAC
1 GTGGCCGGTG-TTGCCGGGCATCTCCA-ATCGC
*
12791 ATGGCCGGTGTTGCGCGGGCATCTCCAAGTCGC
1 GTGGCCGGTGTTGC-CGGGCATCTCCAA-TCGC
12824 GTGGCCGG
1 GTGGCCGG
12832 ATCTCCAAGT
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
32 7 0.12
33 53 0.88
ACGTcount: A:0.10, C:0.30, G:0.40, T:0.20
Consensus pattern (31 bp):
GTGGCCGGTGTTGCCGGGCATCTCCAATCGC
Found at i:12837 original size:21 final size:21
Alignment explanation
Indices: 12811--12852 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
12801 TTGCGCGGGC
*
12811 ATCTCCAAGTCGCGTGGCCGG
1 ATCTCCAAGTCGCATGGCCGG
12832 ATCTCCAAGTCGCATGGCCGG
1 ATCTCCAAGTCGCATGGCCGG
12853 TAACTTGTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.17, C:0.33, G:0.31, T:0.19
Consensus pattern (21 bp):
ATCTCCAAGTCGCATGGCCGG
Found at i:13498 original size:12 final size:12
Alignment explanation
Indices: 13483--13519 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
13473 GACCGGGCAA
*
13483 CGCATGGGGCAT
1 CGCATGGGCCAT
*
13495 CGCACGGGCCAT
1 CGCATGGGCCAT
13507 CGCATGGGCCAT
1 CGCATGGGCCAT
13519 C
1 C
13520 CGCCCACAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.16, C:0.35, G:0.35, T:0.14
Consensus pattern (12 bp):
CGCATGGGCCAT
Found at i:15167 original size:33 final size:32
Alignment explanation
Indices: 15130--15241 Score: 152
Period size: 33 Copynumber: 3.4 Consensus size: 32
15120 TCCGCGCAAC
* *
15130 ACCGGCCACATGACTTGGAGATGCCCGGCCACC
1 ACCGGCCACATGACTCGG-GATGCCCGGCCACA
*
15163 ACCGGCCACATGACTCGGCCATGCCCGGCCACA
1 ACCGGCCACATGACTCGG-GATGCCCGGCCACA
*
15196 ACCGGCCACATGACTCGGGCATGCCCGGCTACA
1 ACCGGCCACATGACTCGGG-ATGCCCGGCCACA
*
15229 ACTGGCCACATGA
1 ACCGGCCACATGA
15242 TCCTTTAACT
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
33 71 1.00
ACGTcount: A:0.22, C:0.40, G:0.26, T:0.12
Consensus pattern (32 bp):
ACCGGCCACATGACTCGGGATGCCCGGCCACA
Found at i:16108 original size:12 final size:13
Alignment explanation
Indices: 16091--16119 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
16081 CTGGTCGAAA
16091 TTTTTTTTTA-AT
1 TTTTTTTTTATAT
16103 TTTTTTTTTATAT
1 TTTTTTTTTATAT
16116 TTTT
1 TTTT
16120 CGATATAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTTTTTATAT
Found at i:19848 original size:11 final size:10
Alignment explanation
Indices: 19830--19863 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
19820 AATTGTCTTC
19830 AAATCTTCAA
1 AAATCTTCAA
19840 AATATCTTCAA
1 AA-ATCTTCAA
19851 GAAATCTTCAA
1 -AAATCTTCAA
19862 AA
1 AA
19864 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:22488 original size:21 final size:21
Alignment explanation
Indices: 22466--22523 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
22456 TACGGACATA
22466 TTCCTATATGCTACGAGCTTAT
1 TTCC-ATATGCTACGAGCTTAT
* *
22488 TTGCATTTGCTACGAGCTTTAT
1 TTCCATATGCTACGAGC-TTAT
* *
22510 TTACATTTGCTACG
1 TTCCATATGCTACG
22524 GACATTATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
21 12 0.38
22 20 0.62
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.43
Consensus pattern (21 bp):
TTCCATATGCTACGAGCTTAT
Found at i:22516 original size:22 final size:21
Alignment explanation
Indices: 22474--22523 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 21
22464 TATTCCTATA
*
22474 TGCTACGAGCTTATTTGCATT
1 TGCTACGAGCTTATTTACATT
22495 TGCTACGAGCTTTATTTACATT
1 TGCTACGAGC-TTATTTACATT
22517 TGCTACG
1 TGCTACG
22524 GACATTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (21 bp):
TGCTACGAGCTTATTTACATT
Found at i:22531 original size:22 final size:22
Alignment explanation
Indices: 22474--22533 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
22464 TATTCCTATA
*
22474 TGCTACGAGC-TTATTTGCATT
1 TGCTACGAGCATTATTTACATT
*
22495 TGCTACGAGCTTTATTTACATT
1 TGCTACGAGCATTATTTACATT
22517 TGCTACG-GACATTATTT
1 TGCTACGAG-CATTATTT
22534 TAGGGTCAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
21 11 0.31
22 24 0.69
ACGTcount: A:0.22, C:0.18, G:0.17, T:0.43
Consensus pattern (22 bp):
TGCTACGAGCATTATTTACATT
Found at i:27524 original size:21 final size:22
Alignment explanation
Indices: 27486--27528 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
27476 GCATGGGCAA
*
27486 GGCCGGGTCATGCGATGGTGAT
1 GGCCGGGTCATGCAATGGTGAT
27508 GGCCGGG-CATGCAATGGTGAT
1 GGCCGGGTCATGCAATGGTGAT
27529 CAGACCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.16, C:0.19, G:0.44, T:0.21
Consensus pattern (22 bp):
GGCCGGGTCATGCAATGGTGAT
Found at i:30803 original size:21 final size:21
Alignment explanation
Indices: 30764--30812 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
30754 TCAATGCTTT
**
30764 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
30786 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
30807 A-GAAGC
1 AGGAAGC
30813 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.