Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006705.1 Corchorus capsularis cultivar CVL-1 contig06726, 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: 11380
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:1152 original size:31 final size:30
Alignment explanation
Indices: 1107--1165 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
1097 CCGTTATAAA
* * * *
1107 AAAATGTCGTTATTTTGCGGCGTCTTAGATT
1 AAAACGTCGCTATTTAGAGGCGT-TTAGATT
1138 AAAACGTCGCTATTTAGAGGCGTTTAGA
1 AAAACGTCGCTATTTAGAGGCGTTTAGA
1166 CGCCGTCATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 5 0.21
31 19 0.79
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.36
Consensus pattern (30 bp):
AAAACGTCGCTATTTAGAGGCGTTTAGATT
Found at i:1687 original size:16 final size:15
Alignment explanation
Indices: 1641--1687 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
1631 AAAAAAAGAA
1641 AGAAGTATAAAATTTC
1 AGAA-TATAAAATTTC
1657 AG-ATATAGAAA-TTC
1 AGAATATA-AAATTTC
1671 AGAACTATAAAATTTC
1 AGAA-TATAAAATTTC
1687 A
1 A
1688 TGTAAGTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
14 9 0.33
15 8 0.30
16 10 0.37
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.30
Consensus pattern (15 bp):
AGAATATAAAATTTC
Found at i:3707 original size:11 final size:11
Alignment explanation
Indices: 3683--3717 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
3673 TTGACAGCGC
3683 AACAAAAACAA
1 AACAAAAACAA
* *
3694 AACGAAAACGA
1 AACAAAAACAA
3705 AACAAAAACAA
1 AACAAAAACAA
3716 AA
1 AA
3718 AATAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:4285 original size:21 final size:21
Alignment explanation
Indices: 4259--4302 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
4249 ATTTAGGGGG
*
4259 TTGCTAAAT-ACCGCCCTATTT
1 TTGCT-AATCACCGCCCCATTT
*
4280 TTGCTATTCACCGCCCCATTT
1 TTGCTAATCACCGCCCCATTT
4301 TT
1 TT
4303 TACACTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.18, C:0.32, G:0.09, T:0.41
Consensus pattern (21 bp):
TTGCTAATCACCGCCCCATTT
Found at i:4519 original size:35 final size:33
Alignment explanation
Indices: 4475--4561 Score: 102
Period size: 35 Copynumber: 2.6 Consensus size: 33
4465 TACTACCGGT
* *
4475 GCCGCCCCAGGGGGGCGGTCTATCCATGGTAGG
1 GCCGCCCCAGGGGGGCGGCCTAGCCATGGTAGG
* * *
4508 GCCGCGCCCCAGGGAGGCGGCCTGGCCATGGTAGT
1 G-C-CGCCCCAGGGGGGCGGCCTAGCCATGGTAGG
*
4543 GCCGCCCCAGGGGGACGGC
1 GCCGCCCCAGGGGGGCGGC
4562 ACCGGTGGGG
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
33 16 0.36
34 2 0.04
35 27 0.60
ACGTcount: A:0.11, C:0.34, G:0.44, T:0.10
Consensus pattern (33 bp):
GCCGCCCCAGGGGGGCGGCCTAGCCATGGTAGG
Found at i:4736 original size:33 final size:32
Alignment explanation
Indices: 4643--4779 Score: 116
Period size: 32 Copynumber: 4.2 Consensus size: 32
4633 CCGTCCCACC
* * * * **
4643 GGGGTGGCCTGTCGTGGCGAAGCCGCCCCACC
1 GGGGCGGCCTGCCCTGGTGAAGCCGCCCCAGT
*
4675 GGGACGGCCTGCCCTGGCT-AAGCCGCCCCAGT
1 GGGGCGGCCTGCCCTGG-TGAAGCCGCCCCAGT
4707 GGGGCGGCCTGCCCATGGTGAAGCCGCCCCA-T
1 GGGGCGGCCTGCCC-TGGTGAAGCCGCCCCAGT
* * * * * *
4739 GAGGGCAGCTTGCCGTGGCGAAGCCTCCCAAGT
1 G-GGGCGGCCTGCCCTGGTGAAGCCGCCCCAGT
4772 GGGGCGGC
1 GGGGCGGC
4780 TTCGCCACGG
Statistics
Matches: 85, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
32 59 0.69
33 26 0.31
ACGTcount: A:0.12, C:0.36, G:0.39, T:0.12
Consensus pattern (32 bp):
GGGGCGGCCTGCCCTGGTGAAGCCGCCCCAGT
Found at i:7060 original size:45 final size:44
Alignment explanation
Indices: 7009--7097 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 44
6999 TAATAGAGTA
*
7009 GTGGAATTATTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG
1 GTGGAATTACTAAAAGATCCCTA-CCCGAATTAATGATAAGCTGG
* *
7054 GTGGAATTACTAAAAGATCCCTACCCGGATTAATGATGAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCGAATTAATGATAAGCTGG
7098 AGAAGTAATC
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 19 0.46
45 22 0.54
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (44 bp):
GTGGAATTACTAAAAGATCCCTACCCGAATTAATGATAAGCTGG
Found at i:7442 original size:166 final size:167
Alignment explanation
Indices: 7151--7481 Score: 459
Period size: 166 Copynumber: 2.0 Consensus size: 167
7141 AATGTCCTAA
* * * * * ** * *
7151 ACTTTAATAGAGTAGTGGAATTACTAAAAGATCCCTACCAAGGCTTGCTTTTGGAGTTAGATAAC
1 ACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCCACCAAGGATTGATGATGGAGCTAGAGAAC
* * *
7216 TTATTTTTCTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTAATTCTTGAGAG
66 TAAATTTTCTCGTCTTTACCTACTTGGCAGATTACTTAAATGTCCTAACTTTTAATTCTTGAGAG
* *
7281 GATTAAATAAGTAATCTTTTTGATCATTTCTCAATGG
131 GATTAAATAACTAAACTTTTTGATCATTTCTCAATGG
* *
7318 ACTTGAATAGAGTAGTGGAATTAATAAAGGATCCCCATCAAGGATTGATGAT-GAGCTAGAGAAC
1 ACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCCACCAAGGATTGATGATGGAGCTAGAGAAC
* * *
7382 TAACATTTT-TCGTCTTTACCTACTTGGCAGATTACTTAAATGTCCTAATTTTTTATTCTTGAGG
66 TAA-ATTTTCTCGTCTTTACCTACTTGGCAGATTACTTAAATGTCCTAACTTTTAATTCTTGAGA
*
7446 GGATTAAATAACTAAACTTTTTGGTCATTTCTCAAT
130 GGATTAAATAACTAAACTTTTTGATCATTTCTCAAT
7482 TGACAAATGA
Statistics
Matches: 143, Mismatches: 20, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
166 96 0.67
167 47 0.33
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.38
Consensus pattern (167 bp):
ACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCCACCAAGGATTGATGATGGAGCTAGAGAAC
TAAATTTTCTCGTCTTTACCTACTTGGCAGATTACTTAAATGTCCTAACTTTTAATTCTTGAGAG
GATTAAATAACTAAACTTTTTGATCATTTCTCAATGG
Found at i:10872 original size:41 final size:42
Alignment explanation
Indices: 10758--11368 Score: 233
Period size: 41 Copynumber: 14.8 Consensus size: 42
10748 TTCCCAGTCA
* * * * *
10758 GAAGTTGTTGTTTTGTTTTCCTAGTGTGCCCTTCCCC-GTCG
1 GAAGGTGTTGTTTAGTTCTCCTAGTTTGCCCTTCCCCACTCG
*
10799 GAAAGTGTTGTTTA-----CC-AGTTTGCCCTTCCCCACT-G
1 GAAGGTGTTGTTTAGTTCTCCTAGTTTGCCCTTCCCCACTCG
*
10834 GAAGGTGTTGTCTAGTTCTCCTAGTTTGCCCTTCCCCAC-CG
1 GAAGGTGTTGTTTAGTTCTCCTAGTTTGCCCTTCCCCACTCG
* * * * * *
10875 GGAGGTGTTGTCTAGTTGCCAATTCCCAGCTTGCCCTT-TCCAGTCG
1 GAAGGTGTTGTTTAGTT--C---TCCTAGTTTGCCCTTCCCCACTCG
* * ** *
10921 GAAGGTGTTTTTTAGTTTTCCTAGGGTGCCCTTCCCC-GTCG
1 GAAGGTGTTGTTTAGTTCTCCTAGTTTGCCCTTCCCCACTCG
* * * *
10962 GAAGATGTTGTTTA------CTAGTTTGCACTTCCCAACT-A
1 GAAGGTGTTGTTTAGTTCTCCTAGTTTGCCCTTCCCCACTCG
** * * * *
10997 GAAAATGTTGGTTAGCTCTCCTAATTTGCCCTTCCCTAC-CAG
1 GAAGGTGTTGTTTAGTTCTCCTAGTTTGCCCTTCCCCACTC-G
* * *** * ** * * **
11039 G-AGGTAAATTCTATTTGACAACTCCCAACTTGCCTTTCCACTGTCG
1 GAAGGT---GT-TGTTT-AGTTCTCCTAGTTTGCCCTTCCCCACTCG
*
11085 GAAGGTGTTGTTTAGATT-TCCTAGTTTGCCCTTCCCC-GTCG
1 GAAGGTGTTGTTTAG-TTCTCCTAGTTTGCCCTTCCCCACTCG
* * * * *
11126 GAAGGTGTTGTTTAGTTTTCCCATTTTGCCC-TACCCAATCG
1 GAAGGTGTTGTTTAGTTCTCCTAGTTTGCCCTTCCCCACTCG
* **
11167 GAAGGGGTTGTTTGAAG-TC-CC-AGTTTGCCCTTCCCTGC-CG
1 GAAGGTGTTGTTT--AGTTCTCCTAGTTTGCCCTTCCCCACTCG
* * * *
11207 AAAGGTGTCGTTTAGCTCTCCTAGTTTGCCCTTACCCACT-G
1 GAAGGTGTTGTTTAGTTCTCCTAGTTTGCCCTTCCCCACTCG
* * * * * *
11248 GAAGGTGTTGTCTAATTGCCAATTCCCAGCTTGCCC-TCCGCAGTCG
1 GAAGGTGTTGTTTAGTT--C---TCCTAGTTTGCCCTTCCCCACTCG
* *
11294 GAAGGTGTTAG-TTAGTTTTCCTAGTTTGCCCTTCCCC-GTCG
1 GAAGGTGTT-GTTTAGTTCTCCTAGTTTGCCCTTCCCCACTCG
* * * *
11335 GAAGGTGTTGATTAGTT-TTCTAATCTGCCCTTCC
1 GAAGGTGTTGTTTAGTTCTCCTAGTTTGCCCTTCC
11369 TCGTCGGAAG
Statistics
Matches: 425, Mismatches: 95, Indels: 101
0.68 0.15 0.16
Matches are distributed among these distances:
35 52 0.12
36 4 0.01
38 2 0.00
39 2 0.00
40 45 0.11
41 198 0.47
42 23 0.05
43 8 0.02
44 2 0.00
45 11 0.03
46 72 0.17
47 6 0.01
ACGTcount: A:0.16, C:0.27, G:0.22, T:0.36
Consensus pattern (42 bp):
GAAGGTGTTGTTTAGTTCTCCTAGTTTGCCCTTCCCCACTCG
Found at i:10984 original size:163 final size:163
Alignment explanation
Indices: 10714--11139 Score: 538
Period size: 163 Copynumber: 2.6 Consensus size: 163
10704 CTCAATCGGA
* * * *
10714 AGGTGTTGTCTAGTTGCCAATTCCCAGCTTGCTCTTCCCAGTCAGAAGTTGTTGTTTT-GTTTTC
1 AGGTGTTGTCTAGTTGCCAATTCCCAGCTTGCCCTTTCCAGTCGGAAGGTGTT-TTTTAGTTTTC
* * * **
10778 CTAGTGTGCCCTTCCCCGTCGGAA-AGTGTTGTTTACCAGTTTGCCCTTCCCCACTGGAAGGTGT
65 CTAGTGTGCCCTTCCCCGTCGGAAGA-TGTTGTTTACCAGTTTGCACTTCCCAACTAGAAAATGT
* * *
10842 T-GTCTAGTTCTCCTAGTTTGCCCTTCCCCACCGGG
129 TGGT-TAGCTCTCCTAATTTGCCCTTCCCCACCAGG
10877 AGGTGTTGTCTAGTTGCCAATTCCCAGCTTGCCCTTTCCAGTCGGAAGGTGTTTTTTAGTTTTCC
1 AGGTGTTGTCTAGTTGCCAATTCCCAGCTTGCCCTTTCCAGTCGGAAGGTGTTTTTTAGTTTTCC
* *
10942 TAGGGTGCCCTTCCCCGTCGGAAGATGTTGTTTACTAGTTTGCACTTCCCAACTAGAAAATGTTG
66 TAGTGTGCCCTTCCCCGTCGGAAGATGTTGTTTACCAGTTTGCACTTCCCAACTAGAAAATGTTG
*
11007 GTTAGCTCTCCTAATTTGCCCTTCCCTACCAGG
131 GTTAGCTCTCCTAATTTGCCCTTCCCCACCAGG
** * * * * * *
11040 AGGTAAAT-TCTATTTGACAACTCCCAACTTG-CCTTTCCACTGTCGGAAGGTGTTGTTTAGATT
1 AGGT-GTTGTCTAGTTGCCAATTCCCAGCTTGCCCTTTCCA--GTCGGAAGGTGTTTTTTAGTTT
* *
11103 TCCTAGTTTGCCCTTCCCCGTCGGAAGGTGTTGTTTA
63 TCCTAGTGTGCCCTTCCCCGTCGGAAGATGTTGTTTA
11140 GTTTTCCCAT
Statistics
Matches: 231, Mismatches: 26, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
162 12 0.05
163 161 0.70
164 58 0.25
ACGTcount: A:0.16, C:0.26, G:0.22, T:0.36
Consensus pattern (163 bp):
AGGTGTTGTCTAGTTGCCAATTCCCAGCTTGCCCTTTCCAGTCGGAAGGTGTTTTTTAGTTTTCC
TAGTGTGCCCTTCCCCGTCGGAAGATGTTGTTTACCAGTTTGCACTTCCCAACTAGAAAATGTTG
GTTAGCTCTCCTAATTTGCCCTTCCCCACCAGG
Found at i:11212 original size:81 final size:83
Alignment explanation
Indices: 11082--11258 Score: 216
Period size: 81 Copynumber: 2.2 Consensus size: 83
11072 CTTTCCACTG
** * * * * * *
11082 TCGGAAGGTGTTGTTTAGATTTCCTAGTTTGCCCTTCCCCGTCGGAAGGTGTTGTTTAGTTTTCC
1 TCGGAAGGTGTTGTTTAGAAGTCCCAGTTTGCCCTTCCCCGCCGAAAGGTGTCGTTTAGCTCTCC
*
11147 CATTTTGCCC-TACCCAA
66 CAGTTTGCCCTTACCCAA
* *
11164 TCGGAAGGGGTTGTTT-GAAGTCCCAGTTTGCCCTTCCCTGCCGAAAGGTGTCGTTTAGCTCTCC
1 TCGGAAGGTGTTGTTTAGAAGTCCCAGTTTGCCCTTCCCCGCCGAAAGGTGTCGTTTAGCTCTCC
* *
11228 TAGTTTGCCCTTACCCAC
66 CAGTTTGCCCTTACCCAA
11246 T-GGAAGGTGTTGT
1 TCGGAAGGTGTTGT
11259 CTAATTGCCA
Statistics
Matches: 80, Mismatches: 14, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
81 58 0.73
82 22 0.28
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.36
Consensus pattern (83 bp):
TCGGAAGGTGTTGTTTAGAAGTCCCAGTTTGCCCTTCCCCGCCGAAAGGTGTCGTTTAGCTCTCC
CAGTTTGCCCTTACCCAA
Found at i:11375 original size:40 final size:41
Alignment explanation
Indices: 11290--11380 Score: 132
Period size: 40 Copynumber: 2.2 Consensus size: 41
11280 GCCCTCCGCA
* *
11290 GTCGGAAGGTGTTAGTTAGTTTTCCTAGTTTGCCCTTCCCC
1 GTCGGAAGGTGTTAGTTAGTTTTCCTAATCTGCCCTTCCCC
*
11331 GTCGGAAGGTGTT-GATTAGTTTT-CTAATCTGCCCTTCCTC
1 GTCGGAAGGTGTTAG-TTAGTTTTCCTAATCTGCCCTTCCCC
11371 GTCGGAAGGT
1 GTCGGAAGGT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
40 25 0.54
41 21 0.46
ACGTcount: A:0.14, C:0.22, G:0.26, T:0.37
Consensus pattern (41 bp):
GTCGGAAGGTGTTAGTTAGTTTTCCTAATCTGCCCTTCCCC
Done.