Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013700.1 Corchorus capsularis cultivar CVL-1 contig13721, 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: 94439
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:10467 original size:57 final size:59
Alignment explanation
Indices: 10404--10530 Score: 204
Period size: 57 Copynumber: 2.1 Consensus size: 59
10394 AACTTCTTGA
*
10404 CATACTTATATTAGTACTATATATAATCTTGTTTTGATCATG-C-TCATGAATACTATG
1 CATACTTATATTAGTACAATATATAATCTTGTTTTGATCATGCCATCATGAATACTATG
10461 CATACTTATATTAGTACAATATATAATCTTGTTTTGATCATGCTCAATTCATGAATACTATG
1 CATACTTATATTAGTACAATATATAATCTTGTTTTGATCATGC-C-A-TCATGAATACTATG
10523 CATACTTA
1 CATACTTA
10531 ACCTTCTGCA
Statistics
Matches: 64, Mismatches: 1, Indels: 5
0.91 0.01 0.07
Matches are distributed among these distances:
57 41 0.64
59 1 0.02
62 22 0.34
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (59 bp):
CATACTTATATTAGTACAATATATAATCTTGTTTTGATCATGCCATCATGAATACTATG
Found at i:12702 original size:11 final size:11
Alignment explanation
Indices: 12686--12711 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
12676 AATTGTGTTC
12686 GACCCAAAGTT
1 GACCCAAAGTT
12697 GACCCAAAGTT
1 GACCCAAAGTT
12708 GACC
1 GACC
12712 TACAATGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.31, G:0.19, T:0.15
Consensus pattern (11 bp):
GACCCAAAGTT
Found at i:14532 original size:21 final size:19
Alignment explanation
Indices: 14507--14564 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
14497 GCTGCTCTAA
*
14507 TAATCTCATTTGTACAGTACC
1 TAATCTCATATGTACAGT--C
* * *
14528 TAATCTAATATGTATAGTG
1 TAATCTCATATGTACAGTC
*
14547 TAATCTCATCTGTACAGT
1 TAATCTCATATGTACAGT
14565 TGCTAAACAG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
19 15 0.50
21 15 0.50
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (19 bp):
TAATCTCATATGTACAGTC
Found at i:15981 original size:1 final size:1
Alignment explanation
Indices: 15975--16028 Score: 90
Period size: 1 Copynumber: 54.0 Consensus size: 1
15965 CCTGGTTTGC
* *
15975 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
16029 CTTTCTTTCT
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:0.00, C:0.02, G:0.02, T:0.96
Consensus pattern (1 bp):
T
Found at i:28623 original size:12 final size:12
Alignment explanation
Indices: 28606--28632 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
28596 ATGTTCAGCC
28606 CTTTTATAATGA
1 CTTTTATAATGA
28618 CTTTTATAATGA
1 CTTTTATAATGA
28630 CTT
1 CTT
28633 AGTACTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (12 bp):
CTTTTATAATGA
Found at i:35592 original size:2 final size:2
Alignment explanation
Indices: 35585--35616 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
35575 TAGGCATCAA
35585 AT AT AT AT AT AT AT AT 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
35617 TTTTTTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46068 original size:22 final size:23
Alignment explanation
Indices: 46045--46090 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
46035 ATAGGTTCGG
*
46045 ATCATTTATTACTTGCATTTGGATA
1 ATCATTTATCACTTGCATTTGG--A
46070 ATCATTTATCACTTGCATTTG
1 ATCATTTATCACTTGCATTTG
46091 TTTGGATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.11, T:0.48
Consensus pattern (23 bp):
ATCATTTATCACTTGCATTTGGA
Found at i:60323 original size:28 final size:28
Alignment explanation
Indices: 60283--60341 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
60273 TTGCATAATC
60283 TATCAAAAATTTGCACGAGTGCCCAAAA
1 TATCAAAAATTTGCACGAGTGCCCAAAA
60311 TATCAAAAATTTGCACGAGTGCCCAAAA
1 TATCAAAAATTTGCACGAGTGCCCAAAA
60339 TAT
1 TAT
60342 TATCATGACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (28 bp):
TATCAAAAATTTGCACGAGTGCCCAAAA
Found at i:61886 original size:28 final size:28
Alignment explanation
Indices: 61854--61910 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
61844 ATTAGTAATC
61854 ACATTAGACACCAATTAATTTAAAGTCA
1 ACATTAGACACCAATTAATTTAAAGTCA
61882 ACATTAGACACCAATTAATTTAAAGTCA
1 ACATTAGACACCAATTAATTTAAAGTCA
61910 A
1 A
61911 GTCGGATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.47, C:0.18, G:0.07, T:0.28
Consensus pattern (28 bp):
ACATTAGACACCAATTAATTTAAAGTCA
Found at i:62613 original size:10 final size:10
Alignment explanation
Indices: 62598--62630 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
62588 TGGAATTTTG
62598 CAATTTGCTT
1 CAATTTGCTT
62608 CAATTTGCTT
1 CAATTTGCTT
62618 CAATTTGCTT
1 CAATTTGCTT
62628 CAA
1 CAA
62631 CTCTAACCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.24, C:0.21, G:0.09, T:0.45
Consensus pattern (10 bp):
CAATTTGCTT
Found at i:63230 original size:115 final size:115
Alignment explanation
Indices: 63020--63236 Score: 321
Period size: 115 Copynumber: 1.9 Consensus size: 115
63010 ATATCGGGTT
* ** *
63020 TAGAAAATTGTTGGATAATTATTGAATTGGGAATATGAAAAGAGAAGAGAAGATGAAAAAAAGAT
1 TAGAAAATTGTTGGACAATTATTGAATCAGGAATATGAAAAGAAAAGAGAAGATGAAAAAAAGAT
63085 TTGGATGGTCTAATCATGGTGCTATGAGGAAAAAGGTAAATTATAATAGG
66 TTGGATGGTCTAATCATGGTGCTATGAGGAAAAAGGTAAATTATAATAGG
* * * *
63135 TAGAAAATTGTTGGACAATTATTGAATCAGGAACT-TGACATGAAAAGGGAAGATG-AAAACAGA
1 TAGAAAATTGTTGGACAATTATTGAATCAGGAA-TATGAAAAGAAAAGAGAAGATGAAAAAAAGA
*
63198 TTTGGATGGTCTAATCATGGTGCTATATAGGAAAAAGGT
65 TTTGGATGGTCTAATCATGGTGCTAT-GAGGAAAAAGGT
63237 CAATCAATAG
Statistics
Matches: 91, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
114 33 0.36
115 57 0.63
116 1 0.01
ACGTcount: A:0.42, C:0.05, G:0.26, T:0.27
Consensus pattern (115 bp):
TAGAAAATTGTTGGACAATTATTGAATCAGGAATATGAAAAGAAAAGAGAAGATGAAAAAAAGAT
TTGGATGGTCTAATCATGGTGCTATGAGGAAAAAGGTAAATTATAATAGG
Found at i:69215 original size:41 final size:41
Alignment explanation
Indices: 69170--69368 Score: 253
Period size: 41 Copynumber: 4.8 Consensus size: 41
69160 ACATCTTCGA
69170 ATAAATTTAAAAAATACCAAGGATCATGTAATGTATAAAGT
1 ATAAATTTAAAAAATACCAAGGATCATGTAATGTATAAAGT
* *
69211 ATAAA-CT--AAAATACCAAGGATCATGTAAGGTATAAAGT
1 ATAAATTTAAAAAATACCAAGGATCATGTAATGTATAAAGT
* *
69249 ATAAATTTAAAAAATACCGAGGATCATATAATGTATAAAGT
1 ATAAATTTAAAAAATACCAAGGATCATGTAATGTATAAAGT
* *
69290 ACCGAGATAAATTT-AAAAATACCGAGGATCATGTAATGTATGAAGT
1 ------ATAAATTTAAAAAATACCAAGGATCATGTAATGTATAAAGT
*
69336 ATAAATTTAAAAAATATCAAGGATCATGTAATG
1 ATAAATTTAAAAAATACCAAGGATCATGTAATG
69369 CCATCAGGCA
Statistics
Matches: 138, Mismatches: 10, Indels: 20
0.82 0.06 0.12
Matches are distributed among these distances:
38 35 0.25
39 1 0.01
40 9 0.07
41 55 0.40
46 30 0.22
47 8 0.06
ACGTcount: A:0.49, C:0.09, G:0.15, T:0.28
Consensus pattern (41 bp):
ATAAATTTAAAAAATACCAAGGATCATGTAATGTATAAAGT
Found at i:69293 original size:26 final size:26
Alignment explanation
Indices: 69263--69336 Score: 70
Period size: 26 Copynumber: 3.1 Consensus size: 26
69253 ATTTAAAAAA
69263 TACCGAGGATCATATAATGTATAAAG
1 TACCGAGGATCATATAATGTATAAAG
* *
69289 TACCGA-G---ATA-AATTTA-AAAA
1 TACCGAGGATCATATAATGTATAAAG
* *
69309 TACCGAGGATCATGTAATGTATGAAG
1 TACCGAGGATCATATAATGTATAAAG
69335 TA
1 TA
69337 TAAATTTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
20 9 0.25
21 6 0.17
22 3 0.08
24 2 0.06
25 6 0.17
26 10 0.28
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.27
Consensus pattern (26 bp):
TACCGAGGATCATATAATGTATAAAG
Found at i:69368 original size:87 final size:79
Alignment explanation
Indices: 69170--69368 Score: 263
Period size: 87 Copynumber: 2.4 Consensus size: 79
69160 ACATCTTCGA
69170 ATAAATTTAAAAAATACCAAGGATCATGTAATGTATAAAGTATAAACTAAAATACCAAGGATCAT
1 ATAAATTTAAAAAATACCAAGGATCATGTAATGTATAAAGTATAAACTAAAATACCAAGGATCAT
69235 GTAAGGTATAAAGT
66 GTAAGGTATAAAGT
* * * *
69249 ATAAATTTAAAAAATACCGAGGATCATATAATGTATAAAGTACCGAGATAAATTTAAAAATACCG
1 ATAAATTTAAAAAATACCAAGGATCATGTAATGTATAAAGT------ATAAA-CT-AAAATACCA
* *
69314 AGGATCATGTAATGTATGAAGT
58 AGGATCATGTAAGGTATAAAGT
*
69336 ATAAATTTAAAAAATATCAAGGATCATGTAATG
1 ATAAATTTAAAAAATACCAAGGATCATGTAATG
69369 CCATCAGGCA
Statistics
Matches: 103, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
79 39 0.38
85 5 0.05
86 1 0.01
87 58 0.56
ACGTcount: A:0.49, C:0.09, G:0.15, T:0.28
Consensus pattern (79 bp):
ATAAATTTAAAAAATACCAAGGATCATGTAATGTATAAAGTATAAACTAAAATACCAAGGATCAT
GTAAGGTATAAAGT
Found at i:69537 original size:35 final size:36
Alignment explanation
Indices: 69476--69549 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 36
69466 TGTTTGTAAT
69476 TTGTTTGTTTGTGTATATTTGTTAGTTAGGTGGTTTA
1 TTGTTTGTTTGTG-ATATTTGTTAGTTAGGTGGTTTA
69513 TTGTTTGTTTGTG-TATTTGTTAGTTAGGTGGTTTA
1 TTGTTTGTTTGTGATATTTGTTAGTTAGGTGGTTTA
69548 TT
1 TT
69550 TAGAGCATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
35 24 0.65
37 13 0.35
ACGTcount: A:0.12, C:0.00, G:0.27, T:0.61
Consensus pattern (36 bp):
TTGTTTGTTTGTGATATTTGTTAGTTAGGTGGTTTA
Found at i:73681 original size:17 final size:18
Alignment explanation
Indices: 73643--73680 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
73633 TAATTTTGAT
*
73643 AAATCTAAGGGTCCAAAA
1 AAATCTAACGGTCCAAAA
73661 AAATCTAACGGTCCAAAA
1 AAATCTAACGGTCCAAAA
73679 AA
1 AA
73681 TGTATAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.18, G:0.13, T:0.16
Consensus pattern (18 bp):
AAATCTAACGGTCCAAAA
Found at i:73823 original size:4 final size:4
Alignment explanation
Indices: 73808--73847 Score: 52
Period size: 4 Copynumber: 11.0 Consensus size: 4
73798 ATAAGCAGAG
73808 AGAA AG-A A-AA AGAA AGAA AGAA AGAA AG-A AG-A AGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
73848 TGGTGTCGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
3 10 0.30
4 23 0.70
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:73829 original size:18 final size:18
Alignment explanation
Indices: 73808--73847 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
73798 ATAAGCAGAG
73808 AGAAAGAAA-AAGAAAGAA
1 AGAAAGAAAGAAG-AAGAA
73826 AGAAAGAAAGAAGAAGAA
1 AGAAAGAAAGAAGAAGAA
73844 AGAA
1 AGAA
73848 TGGTGTCGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (18 bp):
AGAAAGAAAGAAGAAGAA
Found at i:75493 original size:29 final size:28
Alignment explanation
Indices: 75426--75506 Score: 108
Period size: 29 Copynumber: 2.8 Consensus size: 28
75416 GCTTAATACC
*
75426 CAAATTAGCCCCTTAACTATTCATTTTGGGA
1 CAAATTGGCCCCTTAACT-TT--TTTTGGGA
*
75457 CAAATTGGCCCTTTAACTTTTTTTGGGAA
1 CAAATTGGCCCCTTAACTTTTTTTGGG-A
75486 CAAATTGGCCCCTTAACTTTT
1 CAAATTGGCCCCTTAACTTTT
75507 AAAAACGAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
28 7 0.15
29 21 0.46
30 2 0.04
31 16 0.35
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (28 bp):
CAAATTGGCCCCTTAACTTTTTTTGGGA
Found at i:76235 original size:28 final size:28
Alignment explanation
Indices: 76196--76252 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 28
76186 TCTCGTTTTT
76196 AAAAATTAA-GGGCCAATTTGTCCCAAA
1 AAAAATTAAGGGGCCAATTTGTCCCAAA
76223 AAAAAGTTAAGGGGCCAATTTGTCCCAAA
1 AAAAA-TTAAGGGGCCAATTTGTCCCAAA
76252 A
1 A
76253 TGGATAGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 5 0.18
28 4 0.14
29 19 0.68
ACGTcount: A:0.44, C:0.18, G:0.18, T:0.21
Consensus pattern (28 bp):
AAAAATTAAGGGGCCAATTTGTCCCAAA
Found at i:76274 original size:31 final size:29
Alignment explanation
Indices: 76196--76275 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 29
76186 TCTCGTTTTT
76196 AAAAA-TT-AAGGGCCAATTTGTCCCAAA
1 AAAAAGTTAAAGGGCCAATTTGTCCCAAA
*
76223 AAAAAGTTAAGGGGCCAATTTGTCCCAAA
1 AAAAAGTTAAAGGGCCAATTTGTCCCAAA
* * *
76252 ATGGATAGTTAAAGGGCTAATTTG
1 A--AAAAGTTAAAGGGCCAATTTG
76276 GGTATTAAGC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
27 5 0.11
28 2 0.05
29 20 0.45
31 17 0.39
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (29 bp):
AAAAAGTTAAAGGGCCAATTTGTCCCAAA
Found at i:92130 original size:12 final size:12
Alignment explanation
Indices: 92113--92140 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
92103 TTATAAATAT
92113 ATATCTAATCTA
1 ATATCTAATCTA
92125 ATATCTAATCTA
1 ATATCTAATCTA
92137 ATAT
1 ATAT
92141 ATATATAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (12 bp):
ATATCTAATCTA
Done.