Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011756.1 Corchorus capsularis cultivar CVL-1 contig11777, 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: 58059
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1600 original size:18 final size:18
Alignment explanation
Indices: 1577--1612 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1567 TCTGTCCATT
1577 CATCGAAGGAGTACTTAC
1 CATCGAAGGAGTACTTAC
1595 CATCGAAGGAGTACTTAC
1 CATCGAAGGAGTACTTAC
1613 ACTGCAACAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (18 bp):
CATCGAAGGAGTACTTAC
Found at i:13313 original size:27 final size:27
Alignment explanation
Indices: 13279--13357 Score: 158
Period size: 27 Copynumber: 2.9 Consensus size: 27
13269 TTTCATTCTC
13279 TAATTCCAATAACATACATCTAATCTA
1 TAATTCCAATAACATACATCTAATCTA
13306 TAATTCCAATAACATACATCTAATCTA
1 TAATTCCAATAACATACATCTAATCTA
13333 TAATTCCAATAACATACATCTAATC
1 TAATTCCAATAACATACATCTAATC
13358 CATAGCTATA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.33
Consensus pattern (27 bp):
TAATTCCAATAACATACATCTAATCTA
Found at i:13753 original size:24 final size:24
Alignment explanation
Indices: 13726--13772 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
13716 AAGCGGTGGC
13726 GGTGGCAAGGGAGGCGGAGGAGGT
1 GGTGGCAAGGGAGGCGGAGGAGGT
*
13750 GGTGGCAAGGGCGGCGGAGGAGG
1 GGTGGCAAGGGAGGCGGAGGAGG
13773 AGGAGGTGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.19, C:0.11, G:0.64, T:0.06
Consensus pattern (24 bp):
GGTGGCAAGGGAGGCGGAGGAGGT
Found at i:13795 original size:27 final size:27
Alignment explanation
Indices: 13741--13796 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
13731 CAAGGGAGGC
* *
13741 GGAGGAGGTGGTGGCAAGGGCGGCGGA
1 GGAGGAGGAGGTGGCAAAGGCGGCGGA
* * *
13768 GGAGGAGGAGGTGGGAAAGGTGGGGGA
1 GGAGGAGGAGGTGGCAAAGGCGGCGGA
13795 GG
1 GG
13797 TGGCAGTGCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.21, C:0.05, G:0.66, T:0.07
Consensus pattern (27 bp):
GGAGGAGGAGGTGGCAAAGGCGGCGGA
Found at i:14611 original size:17 final size:17
Alignment explanation
Indices: 14589--14622 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
14579 TCTGCAAATT
*
14589 ACCTGCACCCAAAAACA
1 ACCTGCAACCAAAAACA
14606 ACCTGCAACCAAAAACA
1 ACCTGCAACCAAAAACA
14623 GAAAATCAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.38, G:0.06, T:0.06
Consensus pattern (17 bp):
ACCTGCAACCAAAAACA
Found at i:17116 original size:16 final size:16
Alignment explanation
Indices: 17095--17126 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
17085 TGAAAGACTG
17095 GGTTCATATATCAATA
1 GGTTCATATATCAATA
17111 GGTTCATATATCAATA
1 GGTTCATATATCAATA
17127 TAATAGAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (16 bp):
GGTTCATATATCAATA
Found at i:17422 original size:64 final size:64
Alignment explanation
Indices: 17321--17449 Score: 258
Period size: 64 Copynumber: 2.0 Consensus size: 64
17311 GACTCCTCAT
17321 CCCGCTTGTGTAATTTTACACTGTCACTGTATCAAATAATTACTCTTTATCTATTTGACTGGTG
1 CCCGCTTGTGTAATTTTACACTGTCACTGTATCAAATAATTACTCTTTATCTATTTGACTGGTG
17385 CCCGCTTGTGTAATTTTACACTGTCACTGTATCAAATAATTACTCTTTATCTATTTGACTGGTG
1 CCCGCTTGTGTAATTTTACACTGTCACTGTATCAAATAATTACTCTTTATCTATTTGACTGGTG
17449 C
1 C
17450 AATCATGTCC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (64 bp):
CCCGCTTGTGTAATTTTACACTGTCACTGTATCAAATAATTACTCTTTATCTATTTGACTGGTG
Found at i:20694 original size:25 final size:25
Alignment explanation
Indices: 20665--20716 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
20655 GTCATATCAA
*
20665 ATAATTATAGATAATTACTCTATCT
1 ATAATTATAAATAATTACTCTATCT
20690 ATAATTATAAATAATTACTCTATCT
1 ATAATTATAAATAATTACTCTATCT
20715 AT
1 AT
20717 TTGATTGGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.44
Consensus pattern (25 bp):
ATAATTATAAATAATTACTCTATCT
Found at i:27783 original size:15 final size:14
Alignment explanation
Indices: 27765--27794 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
27755 TTATATAGAC
27765 TTGTGTTATTTCTGA
1 TTGTGTTATTT-TGA
27780 TTGTGTTATTTTGA
1 TTGTGTTATTTTGA
27794 T
1 T
27795 GTTAGTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.13, C:0.03, G:0.20, T:0.63
Consensus pattern (14 bp):
TTGTGTTATTTTGA
Found at i:35550 original size:2 final size:2
Alignment explanation
Indices: 35543--35569 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
35533 AGATCTTGCA
35543 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
35570 GTCCTCTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:38593 original size:1 final size:1
Alignment explanation
Indices: 38587--38613 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
38577 CCTTATTCTG
38587 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
38614 CCCAAACCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:40022 original size:32 final size:32
Alignment explanation
Indices: 39978--40049 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 32
39968 TTCTAAGTTG
* *
39978 ATCCGAACCCGAATCAA-CATGACCTAAATTTA
1 ATCCGAACCCGAATCAATC-CGACCCAAATTTA
*
40010 ATCCGAATCCGAATCAATCCGACCCAAATTTA
1 ATCCGAACCCGAATCAATCCGACCCAAATTTA
*
40042 ACCCGAAC
1 ATCCGAAC
40050 ACGACTTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 33 0.97
33 1 0.03
ACGTcount: A:0.39, C:0.32, G:0.10, T:0.19
Consensus pattern (32 bp):
ATCCGAACCCGAATCAATCCGACCCAAATTTA
Found at i:40082 original size:23 final size:23
Alignment explanation
Indices: 40041--40087 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
40031 ACCCAAATTT
* *
40041 AACCCGAACACGACTTAAATCCG
1 AACCCGAAAACGACTTAAACCCG
40064 AACCCGAAAACGA-TCTAAACCCG
1 AACCCGAAAACGACT-TAAACCCG
40087 A
1 A
40088 TGATCCGAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 20 0.95
ACGTcount: A:0.43, C:0.34, G:0.13, T:0.11
Consensus pattern (23 bp):
AACCCGAAAACGACTTAAACCCG
Found at i:40124 original size:11 final size:11
Alignment explanation
Indices: 40108--40134 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
40098 CCAACCTGAC
40108 CCACCCGATTG
1 CCACCCGATTG
40119 CCACCCGATTG
1 CCACCCGATTG
40130 CCACC
1 CCACC
40135 TCTAATTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.19, C:0.52, G:0.15, T:0.15
Consensus pattern (11 bp):
CCACCCGATTG
Found at i:41639 original size:19 final size:20
Alignment explanation
Indices: 41593--41640 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
41583 TGTGGCACGC
*
41593 CACATGTACCAAAAAGTCGTGC
1 CACATGTACCAAAAA--CGTGA
41615 CACATGTACCAAAAA-GTGA
1 CACATGTACCAAAAACGTGA
41634 CACATGT
1 CACATGT
41641 CACGCCACGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
22 15 0.60
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CACATGTACCAAAAACGTGA
Found at i:41645 original size:53 final size:53
Alignment explanation
Indices: 41560--41662 Score: 161
Period size: 53 Copynumber: 1.9 Consensus size: 53
41550 GACGTGGCAC
* **
41560 GCCACGTGTACCAAAAAGTGACATGTGGCACGCCACATGTACCAAAAAGTCGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT
* *
41613 GCCACATGTACCAAAAAGTGACACATGTCACGCCACGTGTACCAAAAAGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGT
41663 GACACGTGGC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.17
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT
Found at i:41691 original size:31 final size:31
Alignment explanation
Indices: 41612--41683 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
41602 CAAAAAGTCG
* *
41612 TGCCACATGTACCAAAAAGTGACACATGTCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
* *
41643 CGCCACGTGTACCAAAAAGTGACACGTGGCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
41674 TGCCACATGT
1 TGCCACATGT
41684 TTCAAAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.33, C:0.28, G:0.21, T:0.18
Consensus pattern (31 bp):
TGCCACATGTACCAAAAAGTGACACGTGGCA
Found at i:44932 original size:2 final size:2
Alignment explanation
Indices: 44925--44953 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
44915 TGATTTAAAG
44925 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
44954 CATGTGGGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45121 original size:65 final size:65
Alignment explanation
Indices: 45010--45192 Score: 269
Period size: 65 Copynumber: 2.8 Consensus size: 65
45000 TACACATATT
* *
45010 TTTACTAATGTTTCATATGGG-TCAATGGACACTTAATATGGTTTAATCCAATTGAAATGAGCAA
1 TTTACTAATGTTTTATATGGGCTCAATGGACACTTAACATGGTTTAATCCAATTGAAATGAGCAA
* ** * *
45074 TTTACTAATGTTTTATATGGGCTCAATGGACATTTAACATGGTTTAATCCAATTGAGTTGGGCAC
1 TTTACTAATGTTTTATATGGGCTCAATGGACACTTAACATGGTTTAATCCAATTGAAATGAGCAA
* * *
45139 TTTACTAATGTTTTATATGTGCCCAATGGATACTTAACATGGTTTAATCCAATT
1 TTTACTAATGTTTTATATGGGCTCAATGGACACTTAACATGGTTTAATCCAATT
45193 AGGGTGGGCA
Statistics
Matches: 107, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
64 20 0.19
65 87 0.81
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.39
Consensus pattern (65 bp):
TTTACTAATGTTTTATATGGGCTCAATGGACACTTAACATGGTTTAATCCAATTGAAATGAGCAA
Found at i:50104 original size:15 final size:17
Alignment explanation
Indices: 50066--50099 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
50056 TACACCAACC
50066 CATAAATATTATTTTTA
1 CATAAATATTATTTTTA
50083 CTATAAATATTATTTTT
1 C-ATAAATATTATTTTT
50100 CTAAAACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 1 0.06
18 15 0.94
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
CATAAATATTATTTTTA
Found at i:50619 original size:25 final size:25
Alignment explanation
Indices: 50589--50637 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
50579 ATTGTTTATG
* *
50589 GAAAGTAAATCATTATTGCTTGATT
1 GAAAGTAAATAATTATTGATTGATT
50614 GAAAGTAAATAATTATTGATTGAT
1 GAAAGTAAATAATTATTGATTGAT
50638 CATTACTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.41, C:0.04, G:0.16, T:0.39
Consensus pattern (25 bp):
GAAAGTAAATAATTATTGATTGATT
Found at i:52106 original size:23 final size:22
Alignment explanation
Indices: 52071--52122 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
52061 AGAAATTTAA
*
52071 AATAAT-TATGAAAAAAATAAT
1 AATAATATAAGAAAAAAATAAT
* *
52092 GAATGATATAAGAAAAAAGTAAT
1 -AATAATATAAGAAAAAAATAAT
52115 AATAATAT
1 AATAATAT
52123 TTAAAAAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 12 0.48
23 13 0.52
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (22 bp):
AATAATATAAGAAAAAAATAAT
Found at i:53182 original size:21 final size:20
Alignment explanation
Indices: 53148--53187 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
53138 TCTCTTTGTT
*
53148 TTTCTCCTCCTTCTTCTTCA
1 TTTCTCCTCCTTCTGCTTCA
*
53168 TTTCTTCTACCTTCTGCTTC
1 TTTCTCCT-CCTTCTGCTTC
53188 TTCTCCATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.05, C:0.38, G:0.03, T:0.55
Consensus pattern (20 bp):
TTTCTCCTCCTTCTGCTTCA
Found at i:53891 original size:54 final size:54
Alignment explanation
Indices: 53825--53928 Score: 181
Period size: 54 Copynumber: 1.9 Consensus size: 54
53815 TGTTTTTCTC
* *
53825 TATCTTTGAATGTAACTAAGTAATTTTTTCAAAACTGAGTAATTTTTATATCTT
1 TATCTTTGAATGTAACTAAGTAATTTTCTCAAAACTGAGTAATTCTTATATCTT
*
53879 TATCTTTGAATGTAACTGAGTAATTTTCTCAAAACTGAGTAATTCTTATA
1 TATCTTTGAATGTAACTAAGTAATTTTCTCAAAACTGAGTAATTCTTATA
53929 AATGTTTTGT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.45
Consensus pattern (54 bp):
TATCTTTGAATGTAACTAAGTAATTTTCTCAAAACTGAGTAATTCTTATATCTT
Found at i:54181 original size:63 final size:63
Alignment explanation
Indices: 54107--54233 Score: 245
Period size: 63 Copynumber: 2.0 Consensus size: 63
54097 TTATTTCAAA
*
54107 ATTGTAAACCTTTATATCTCATTTATATTTCAAAATTTTGTTAGAAATTTGTGTCTGCAGAGG
1 ATTGTAAACCTTTATATCTCATTTATAATTCAAAATTTTGTTAGAAATTTGTGTCTGCAGAGG
54170 ATTGTAAACCTTTATATCTCATTTATAATTCAAAATTTTGTTAGAAATTTGTGTCTGCAGAGG
1 ATTGTAAACCTTTATATCTCATTTATAATTCAAAATTTTGTTAGAAATTTGTGTCTGCAGAGG
54233 A
1 A
54234 GTTTTGTGTG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.43
Consensus pattern (63 bp):
ATTGTAAACCTTTATATCTCATTTATAATTCAAAATTTTGTTAGAAATTTGTGTCTGCAGAGG
Found at i:54668 original size:22 final size:21
Alignment explanation
Indices: 54614--54668 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
54604 ATCTATGTTT
*
54614 TTGTTATTTTAATATCTCTTA
1 TTGTTTTTTTAATATCTCTTA
*
54635 TT-TCTTAATTTAATATCTCTTTA
1 TTGT-TT-TTTTAATATCTC-TTA
54658 TTGTTTTTTTA
1 TTGTTTTTTTA
54669 GGGATAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
20 1 0.04
21 3 0.11
22 15 0.56
23 7 0.26
24 1 0.04
ACGTcount: A:0.22, C:0.09, G:0.04, T:0.65
Consensus pattern (21 bp):
TTGTTTTTTTAATATCTCTTA
Found at i:55884 original size:22 final size:21
Alignment explanation
Indices: 55830--55884 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
55820 ATCTATGTTT
*
55830 TTGTTATTTTAATATCTCTTA
1 TTGTTTTTTTAATATCTCTTA
*
55851 TT-TCTTAATTTAATATCTCTTTA
1 TTGT-TT-TTTTAATATCTC-TTA
55874 TTGTTTTTTTA
1 TTGTTTTTTTA
55885 GGGATAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
20 1 0.04
21 3 0.11
22 15 0.56
23 7 0.26
24 1 0.04
ACGTcount: A:0.22, C:0.09, G:0.04, T:0.65
Consensus pattern (21 bp):
TTGTTTTTTTAATATCTCTTA
Done.