Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015815.1 Corchorus capsularis cultivar CVL-1 contig15836, 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: 65317
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Found at i:1713 original size:128 final size:128
Alignment explanation
Indices: 1556--1816 Score: 470
Period size: 128 Copynumber: 2.0 Consensus size: 128
1546 ATCATTTGAT
*
1556 AAATAATCCAGAAAAAAAATGATTTGTTTATTGAGAACAGGGCCCACCAATAGTAACTTTGTTCC
1 AAATAATCCAGAAAAAAAATGATTTGTTTATTGAGAACAGGGCCCACAAATAGTAACTTTGTTCC
* *
1621 AAACTTCCCAAAACGCCCTCAACCATCAACTGAAATAACAAAAAAATCAAGCACAAAAGTACCG
66 AAACTTCCCAAAACGCCCTCAACCATCAACCGAAATAAC-AAAAAACCAAGCACAAAAGTACCG
*
1685 AAATAATCCAG-AAAAAAATGATTTGTTTATTGAGAACGGGGCCCACAAATAGTAACTTTGTTCC
1 AAATAATCCAGAAAAAAAATGATTTGTTTATTGAGAACAGGGCCCACAAATAGTAACTTTGTTCC
1749 AAACTTCCCAAAACGCCCTCAACCATCAACCGAAATAACAAAAAACCAAGCACAAAAGTACCG
66 AAACTTCCCAAAACGCCCTCAACCATCAACCGAAATAACAAAAAACCAAGCACAAAAGTACCG
1812 AAATA
1 AAATA
1817 CTCCTGACAA
Statistics
Matches: 128, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
127 28 0.22
128 89 0.70
129 11 0.09
ACGTcount: A:0.45, C:0.23, G:0.12, T:0.20
Consensus pattern (128 bp):
AAATAATCCAGAAAAAAAATGATTTGTTTATTGAGAACAGGGCCCACAAATAGTAACTTTGTTCC
AAACTTCCCAAAACGCCCTCAACCATCAACCGAAATAACAAAAAACCAAGCACAAAAGTACCG
Found at i:3433 original size:46 final size:47
Alignment explanation
Indices: 3354--3457 Score: 138
Period size: 46 Copynumber: 2.2 Consensus size: 47
3344 CACAATTACT
* *
3354 TGGCGCCCGACCACTTACGAAGCCTAGCAACCGACAACATACAAGCC
1 TGGCGCCCGACAACATACGAAGCCTAGCAACCGACAACATACAAGCC
* * * * *
3401 TGGCGCCCGACAACATAC-AAGCCTGGCGACCGACTACTTATAAGCC
1 TGGCGCCCGACAACATACGAAGCCTAGCAACCGACAACATACAAGCC
3447 TGGCGCCCGAC
1 TGGCGCCCGAC
3458 CACTTGCGAC
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
46 34 0.68
47 16 0.32
ACGTcount: A:0.28, C:0.38, G:0.22, T:0.12
Consensus pattern (47 bp):
TGGCGCCCGACAACATACGAAGCCTAGCAACCGACAACATACAAGCC
Found at i:3462 original size:23 final size:23
Alignment explanation
Indices: 3354--3462 Score: 119
Period size: 23 Copynumber: 4.7 Consensus size: 23
3344 CACAATTACT
*
3354 TGGCGCCCGACCACTTACGAAGCC
1 TGGCGCCCGACAACTTAC-AAGCC
* ** *
3378 TAGCAACCGACAACATACAAGCC
1 TGGCGCCCGACAACTTACAAGCC
*
3401 TGGCGCCCGACAACATACAAGCC
1 TGGCGCCCGACAACTTACAAGCC
* * *
3424 TGGCGACCGACTACTTATAAGCC
1 TGGCGCCCGACAACTTACAAGCC
*
3447 TGGCGCCCGACCACTT
1 TGGCGCCCGACAACTT
3463 GCGACCGAAG
Statistics
Matches: 71, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
23 58 0.82
24 13 0.18
ACGTcount: A:0.28, C:0.38, G:0.21, T:0.14
Consensus pattern (23 bp):
TGGCGCCCGACAACTTACAAGCC
Found at i:3632 original size:27 final size:26
Alignment explanation
Indices: 3601--3664 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 26
3591 TACGACCACT
3601 CACGTGACCTCCAAAGGACAACTCCAA
1 CACGTGACCTCCAAAGGACAAC-CCAA
* * *
3628 CACGTGACCTCCGAAGTACAACCCCA
1 CACGTGACCTCCAAAGGACAACCCAA
*
3654 CATGTGACCTC
1 CACGTGACCTC
3665 GCGCGTGCGA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
26 13 0.39
27 20 0.61
ACGTcount: A:0.31, C:0.39, G:0.16, T:0.14
Consensus pattern (26 bp):
CACGTGACCTCCAAAGGACAACCCAA
Found at i:11795 original size:33 final size:33
Alignment explanation
Indices: 11758--11820 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
11748 TCCGGGCGTA
*
11758 GCCGGGCATGGCCATGTCGCGTGGCCGGTGATG
1 GCCGGGCATGGCCATGTCGCATGGCCGGTGATG
* *
11791 GCCGGGCATGTCCATGTTGCATGGCCGGTG
1 GCCGGGCATGGCCATGTCGCATGGCCGGTG
11821 TTCGCGGGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.10, C:0.27, G:0.43, T:0.21
Consensus pattern (33 bp):
GCCGGGCATGGCCATGTCGCATGGCCGGTGATG
Found at i:11854 original size:21 final size:21
Alignment explanation
Indices: 11830--11871 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
11820 GTTCGCGGGC
* **
11830 ATCTGCAAGTCGTGTGGCCGG
1 ATCTCCAAGTCGCATGGCCGG
11851 ATCTCCAAGTCGCATGGCCGG
1 ATCTCCAAGTCGCATGGCCGG
11872 TCACTTGTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.29, G:0.33, T:0.21
Consensus pattern (21 bp):
ATCTCCAAGTCGCATGGCCGG
Found at i:13724 original size:33 final size:32
Alignment explanation
Indices: 13687--13780 Score: 102
Period size: 33 Copynumber: 2.8 Consensus size: 32
13677 CCAAAACAGA
13687 TTTAGTTTCATCACAAACAACACCTAAATTAGG
1 TTTAGTTTCATCACAAACAACA-CTAAATTAGG
*
13720 TTTAGTATCATCA-AAACCAACACTCAAATTAGG
1 TTTAGTTTCATCACAAA-CAACACT-AAATTAGG
* *
13753 TTTAGTATT-TTCGCAAACAACATCTAAA
1 TTTAGT-TTCATCACAAACAACA-CTAAA
13781 ACACTCTTTG
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
32 5 0.10
33 41 0.79
34 6 0.12
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (32 bp):
TTTAGTTTCATCACAAACAACACTAAATTAGG
Found at i:16183 original size:33 final size:33
Alignment explanation
Indices: 16171--16249 Score: 158
Period size: 33 Copynumber: 2.4 Consensus size: 33
16161 GAGTCAAGTG
16171 GCCGGGCATGGCCGAGTCAAGTGTCCGGGCGTA
1 GCCGGGCATGGCCGAGTCAAGTGTCCGGGCGTA
16204 GCCGGGCATGGCCGAGTCAAGTGTCCGGGCGTA
1 GCCGGGCATGGCCGAGTCAAGTGTCCGGGCGTA
16237 GCCGGGCATGGCC
1 GCCGGGCATGGCC
16250 ATGTCGCGTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.14, C:0.29, G:0.43, T:0.14
Consensus pattern (33 bp):
GCCGGGCATGGCCGAGTCAAGTGTCCGGGCGTA
Found at i:16207 original size:23 final size:23
Alignment explanation
Indices: 16145--16200 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
16135 GTGGCCGGTT
16145 GTGGCCGGGCATGGCCGAGTCAA
1 GTGGCCGGGCATGGCCGAGTCAA
16168 GTGGCCGGGCATGGCCGAGTCAA
1 GTGGCCGGGCATGGCCGAGTCAA
*
16191 GTGTCCGGGC
1 GTGGCCGGGC
16201 GTAGCCGGGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.14, C:0.27, G:0.45, T:0.14
Consensus pattern (23 bp):
GTGGCCGGGCATGGCCGAGTCAA
Found at i:16285 original size:33 final size:32
Alignment explanation
Indices: 16237--16328 Score: 103
Period size: 33 Copynumber: 2.8 Consensus size: 32
16227 TCCGGGCGTA
** *
16237 GCCGGGCATGGCCATGTCGCGTGGTCGGTGATG
1 GCCGGGCATCTCCATGTCGCGTGGCCGGTG-TG
* * *
16270 GCCGGGCATCTCCATGTTGCATGGCCGGTGTT
1 GCCGGGCATCTCCATGTCGCGTGGCCGGTGTG
*
16302 GCGCGGGCATCTCCAAGTCGCGTGGCC
1 GC-CGGGCATCTCCATGTCGCGTGGCC
16329 AGGTCTCCAA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
32 3 0.06
33 46 0.94
ACGTcount: A:0.10, C:0.29, G:0.39, T:0.22
Consensus pattern (32 bp):
GCCGGGCATCTCCATGTCGCGTGGCCGGTGTG
Found at i:18501 original size:40 final size:40
Alignment explanation
Indices: 18446--18548 Score: 111
Period size: 40 Copynumber: 2.6 Consensus size: 40
18436 AAAGCAAGAG
* *
18446 AAGAAAGTATCATGTCGACCGACTACAT-CACATTCAAAAC
1 AAGAAAATAACATGTCGACCGACT-CATACACATTCAAAAC
* * *
18486 AAGAAAATACCATGTCGACCGA-TCATACCGCATTCGAAAC
1 AAGAAAATAACATGTCGACCGACTCATA-CACATTCAAAAC
* *
18526 AAGAAAAGAACAAGTCGACCGAC
1 AAGAAAATAACATGTCGACCGAC
18549 CACAACATAT
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
38 3 0.06
39 1 0.02
40 49 0.92
ACGTcount: A:0.44, C:0.25, G:0.16, T:0.16
Consensus pattern (40 bp):
AAGAAAATAACATGTCGACCGACTCATACACATTCAAAAC
Found at i:20735 original size:33 final size:33
Alignment explanation
Indices: 20689--20762 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 33
20679 AGCACTAGTG
* *
20689 ACCGGCCATGCGAC-TCGGAGAAGTCCGGCCA-A
1 ACCGGCCACGCGACAT-GGACAAGTCCGGCCACA
*
20721 CACCGGCCACGCGACATGGACATGTCCGGCCACA
1 -ACCGGCCACGCGACATGGACAAGTCCGGCCACA
20755 ACCGGCCA
1 ACCGGCCA
20763 TCGCTAGGCG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 34 0.94
34 2 0.06
ACGTcount: A:0.24, C:0.39, G:0.28, T:0.08
Consensus pattern (33 bp):
ACCGGCCACGCGACATGGACAAGTCCGGCCACA
Found at i:27222 original size:33 final size:33
Alignment explanation
Indices: 27185--27291 Score: 135
Period size: 33 Copynumber: 3.2 Consensus size: 33
27175 AGCACTAGTG
* *
27185 ACCGGCCATGCGACTTGGAGAAGTCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
* * *
27218 ACCGGCCACGTGACTCGGAGATGCCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
* *
27251 ACCGGCCACGCGACATGGACATGTCCGGCC-AC
1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
27283 AACCGGCCA
1 -ACCGGCCA
27292 TCGCTAGGCG
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
32 2 0.03
33 61 0.97
ACGTcount: A:0.23, C:0.38, G:0.29, T:0.09
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
Found at i:28361 original size:11 final size:10
Alignment explanation
Indices: 28345--28374 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
28335 AGTTATATCG
28345 AAAAATATAAA
1 AAAAATA-AAA
28356 AAAAATAAAA
1 AAAAATAAAA
28366 AAAAATAAA
1 AAAAATAAA
28375 TAAATTTTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 12 0.63
11 7 0.37
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:30724 original size:30 final size:30
Alignment explanation
Indices: 30684--30742 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
30674 TGTCTTCAAG
*
30684 TCCATAATAAGTCCTT-GGCGCATCATTCCT
1 TCCATAATAAG-CCTTGGGCACATCATTCCT
*
30714 TCCATGATAAGCCTTGGGCACATCATTCC
1 TCCATAATAAGCCTTGGGCACATCATTCC
30743 CTCCCCCTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.24, C:0.31, G:0.15, T:0.31
Consensus pattern (30 bp):
TCCATAATAAGCCTTGGGCACATCATTCCT
Found at i:31183 original size:33 final size:33
Alignment explanation
Indices: 31114--31219 Score: 110
Period size: 33 Copynumber: 3.3 Consensus size: 33
31104 TTCTTTTCAC
* * *
31114 CCAAAACAGATTTATTTTCAATG---TCATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
* *
31144 CTAAAACAGGATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
* ** *
31177 CCAAAACACAATTATTTTTAATGCTATGTTCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
31210 CCAAAACAGA
1 CCAAAACAGA
31220 TTTGTTTTCA
Statistics
Matches: 61, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
30 19 0.31
33 42 0.69
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (33 bp):
CCAAAACAGAATTATTTGCAATGCTATGATCAA
Found at i:33839 original size:21 final size:21
Alignment explanation
Indices: 33815--33867 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
33805 CATCGGACCT
33815 AATGGCATCTTCAAAGGATCA
1 AATGGCATCTTCAAAGGATCA
33836 AATGGCATCTTCAAAGGATCA
1 AATGGCATCTTCAAAGGATCA
33857 AATGGCATCTT
1 AATGGCATCTT
33868 AATGGTATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (21 bp):
AATGGCATCTTCAAAGGATCA
Found at i:39038 original size:12 final size:12
Alignment explanation
Indices: 39020--39051 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
39010 GCCGCGCAAC
39020 ACCGGCCACATG
1 ACCGGCCACATG
*
39032 TCCGGCCACATG
1 ACCGGCCACATG
39044 ACCGGCCA
1 ACCGGCCA
39052 TCGCATGCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.22, C:0.44, G:0.25, T:0.09
Consensus pattern (12 bp):
ACCGGCCACATG
Found at i:42565 original size:6 final size:6
Alignment explanation
Indices: 42554--42589 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
42544 ACTTCTTACA
42554 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT
42590 GGGTTGCCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AAAATT
Found at i:50691 original size:33 final size:33
Alignment explanation
Indices: 50534--50688 Score: 208
Period size: 33 Copynumber: 4.7 Consensus size: 33
50524 CGACTTGGAG
* *
50534 ATGCCCGGCCA-ACACCGGTCACGCGACATGACC
1 ATGCCCGGCCACA-ACCGGCCACACGACATGACC
50567 ATGCCCGGCCACAACCGGCCACACGACATGACC
1 ATGCCCGGCCACAACCGGCCACACGACATGACC
50600 ATGCCCGGCCACAACCGGCCACACGACATGACC
1 ATGCCCGGCCACAACCGGCCACACGACATGACC
* * *
50633 ATGCCCGGCCACAACCGGTCACATGAC-TCGGCC
1 ATGCCCGGCCACAACCGGCCACACGACAT-GACC
*
50666 ATGCCCGACCATC-ACCGGCCACA
1 ATGCCCGGCCA-CAACCGGCCACA
50689 TGATCCTTTA
Statistics
Matches: 112, Mismatches: 7, Indels: 6
0.90 0.06 0.05
Matches are distributed among these distances:
32 1 0.01
33 109 0.97
34 2 0.02
ACGTcount: A:0.25, C:0.45, G:0.22, T:0.08
Consensus pattern (33 bp):
ATGCCCGGCCACAACCGGCCACACGACATGACC
Found at i:61011 original size:33 final size:32
Alignment explanation
Indices: 60969--61075 Score: 128
Period size: 33 Copynumber: 3.2 Consensus size: 32
60959 CGACTTGGAG
*
60969 ATGCCCGGCCA-ACACTGGTCACGTGACATGACC
1 ATGCCCGGCCACA-ACCGGTCAC-TGACATGACC
*
61002 ATGCCCGGCCACAACCGGCCACTCGACATGACC
1 ATGCCCGGCCACAACCGGTCACT-GACATGACC
*
61035 ATGCCCGGCCACAACCGGTCACATGA-ATCGGCC
1 ATGCCCGGCCACAACCGGTCAC-TGACAT-GACC
61068 ATGCCCGG
1 ATGCCCGG
61076 TCATCACCGG
Statistics
Matches: 66, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
32 3 0.05
33 61 0.92
34 2 0.03
ACGTcount: A:0.23, C:0.40, G:0.24, T:0.12
Consensus pattern (32 bp):
ATGCCCGGCCACAACCGGTCACTGACATGACC
Found at i:62386 original size:37 final size:38
Alignment explanation
Indices: 62321--62399 Score: 124
Period size: 37 Copynumber: 2.1 Consensus size: 38
62311 CTTATATACT
* *
62321 TGATCAACATACATGTCTTTTCATATAGACATAACTTTA
1 TGATCAACATA-ATGTCTTTCCAAATAGACATAACTTTA
62360 TGATCAACAT-ATGTCTTTCCAAATAGACATAACTTTA
1 TGATCAACATAATGTCTTTCCAAATAGACATAACTTTA
62397 TGA
1 TGA
62400 ATAATTATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 28 0.74
39 10 0.26
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.37
Consensus pattern (38 bp):
TGATCAACATAATGTCTTTCCAAATAGACATAACTTTA
Done.