Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009974.1 Corchorus capsularis cultivar CVL-1 contig09995, 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: 107271
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1285 original size:36 final size:36
Alignment explanation
Indices: 1240--1318 Score: 124
Period size: 36 Copynumber: 2.2 Consensus size: 36
1230 TCGTGTACCT
*
1240 GGCCCAATTGCAGTACCTCTACCT-CTCAATGCACCA
1 GGCCCAATTGCAGCACCTCTACCTAC-CAATGCACCA
1276 GGCCCAATTGCAGCACCTCTACCTACCAATGCACCA
1 GGCCCAATTGCAGCACCTCTACCTACCAATGCACCA
*
1312 GGACCAA
1 GGCCCAA
1319 ATGCCAACGG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
36 39 0.98
37 1 0.03
ACGTcount: A:0.28, C:0.39, G:0.15, T:0.18
Consensus pattern (36 bp):
GGCCCAATTGCAGCACCTCTACCTACCAATGCACCA
Found at i:1566 original size:6 final size:6
Alignment explanation
Indices: 1550--1579 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1540 GGAATTTCAA
*
1550 GTTTAT ATTTAT GTTTAT GTTTAT GTTTAT
1 GTTTAT GTTTAT GTTTAT GTTTAT GTTTAT
1580 ATATATGAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.20, C:0.00, G:0.13, T:0.67
Consensus pattern (6 bp):
GTTTAT
Found at i:1567 original size:12 final size:12
Alignment explanation
Indices: 1550--1586 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
1540 GGAATTTCAA
1550 GTTTATATTTAT
1 GTTTATATTTAT
*
1562 GTTTATGTTTAT
1 GTTTATATTTAT
*
1574 GTTTATATATAT
1 GTTTATATTTAT
1586 G
1 G
1587 AGGAATGACA
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:0.24, C:0.00, G:0.14, T:0.62
Consensus pattern (12 bp):
GTTTATATTTAT
Found at i:7471 original size:31 final size:31
Alignment explanation
Indices: 7395--7478 Score: 89
Period size: 32 Copynumber: 2.7 Consensus size: 31
7385 CGTGGCATGC
* **
7395 CACGTATACCAAAAAATGACATGTGGTACGT
1 CACGTATACCAAAAAGTGACACATGGTACGT
* *
7426 CACGTTTCATCAAAAAGTGACACAT-GTCACGT
1 CACGTAT-ACCAAAAAGTGACACATGGT-ACGT
*
7458 CACGTGTACCAAAAAGTGACA
1 CACGTATACCAAAAAGTGACA
7479 TGCGACGGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
31 21 0.48
32 23 0.52
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (31 bp):
CACGTATACCAAAAAGTGACACATGGTACGT
Found at i:7813 original size:18 final size:18
Alignment explanation
Indices: 7790--7835 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
7780 ATGGAATCTG
*
7790 TTTCATCTTTTACGAAAT
1 TTTCATCTTTTACGAAAC
*
7808 TTTCATCTTTTAGGAAAC
1 TTTCATCTTTTACGAAAC
7826 TTTCATCTTT
1 TTTCATCTTT
7836 AAAGCACCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.24, C:0.17, G:0.07, T:0.52
Consensus pattern (18 bp):
TTTCATCTTTTACGAAAC
Found at i:17682 original size:14 final size:14
Alignment explanation
Indices: 17663--17692 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
17653 GAGTTGGATG
17663 TCCCTTAAATAATA
1 TCCCTTAAATAATA
17677 TCCCTTAAATAATA
1 TCCCTTAAATAATA
17691 TC
1 TC
17693 TCAAATTCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (14 bp):
TCCCTTAAATAATA
Found at i:20136 original size:3 final size:3
Alignment explanation
Indices: 20128--20159 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
20118 ACACAAGTTT
20128 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
20160 TAATCAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:39625 original size:19 final size:19
Alignment explanation
Indices: 39601--39637 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
39591 GTACAGTACC
39601 TAATCTAATCTGTACAGTG
1 TAATCTAATCTGTACAGTG
*
39620 TAATCTCATCTGTACAGT
1 TAATCTAATCTGTACAGT
39638 TACTAAACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (19 bp):
TAATCTAATCTGTACAGTG
Found at i:39765 original size:2 final size:2
Alignment explanation
Indices: 39760--39787 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39750 TTTTACAACG
39760 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
39788 TTATTGATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42138 original size:19 final size:21
Alignment explanation
Indices: 42114--42153 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
42104 ATTTTACAAA
*
42114 GGTCCAGAAAT-T-AACATTT
1 GGTCCACAAATATAAACATTT
42133 GGTCCACAAATATAAACATTT
1 GGTCCACAAATATAAACATTT
42154 TACCCCATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 1 0.06
21 7 0.39
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.30
Consensus pattern (21 bp):
GGTCCACAAATATAAACATTT
Found at i:44485 original size:78 final size:80
Alignment explanation
Indices: 44339--44502 Score: 242
Period size: 78 Copynumber: 2.1 Consensus size: 80
44329 ATTACTAAAT
* ** *
44339 AATACTATATTTTAATTATTTATTTATTTCATTATATTAAAATAATGGAAATTTAAATTATTATC
1 AATAATATATTTTAATTATTTATTTATTTCATTATATTAAAATAATAAAAATTTAAATTATCATC
*
44404 ATTAATTAGGATTTA
66 ATTAATTAGGATCTA
* *
44419 AATAATATATTTTAATTATTTATTTATTTCA-T-TATTAAAATAATAAAAATTTAGATTATCCTC
1 AATAATATATTTTAATTATTTATTTATTTCATTATATTAAAATAATAAAAATTTAAATTATCATC
44482 ATTAATTAGGATCTA
66 ATTAATTAGGATCTA
*
44497 ATTAAT
1 AATAAT
44503 GTGGCCAATA
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
78 45 0.59
79 1 0.01
80 30 0.39
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (80 bp):
AATAATATATTTTAATTATTTATTTATTTCATTATATTAAAATAATAAAAATTTAAATTATCATC
ATTAATTAGGATCTA
Found at i:54997 original size:29 final size:29
Alignment explanation
Indices: 54955--55013 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 29
54945 GAGGAAAATT
54955 TGGAGCAAGGCAG-CTATGACCAATTAATA
1 TGGAGCAAGGCAGCCT-TGACCAATTAATA
54984 TGGAGCAAGGCAGCCTTGACCAATTAATA
1 TGGAGCAAGGCAGCCTTGACCAATTAATA
55013 T
1 T
55014 AAACTTTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 27 0.93
30 2 0.07
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.22
Consensus pattern (29 bp):
TGGAGCAAGGCAGCCTTGACCAATTAATA
Found at i:56634 original size:40 final size:40
Alignment explanation
Indices: 56590--56666 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
56580 AGCTCATTCT
*
56590 TGATAATGATCTTTCATGAATTCATATATGCGTAAACGAA
1 TGATAATGATCTTTCATCAATTCATATATGCGTAAACGAA
*
56630 TGATAATGATCTTTCATCAATTCATATATGGGTAAAC
1 TGATAATGATCTTTCATCAATTCATATATGCGTAAAC
56667 TTATAAGACA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.36
Consensus pattern (40 bp):
TGATAATGATCTTTCATCAATTCATATATGCGTAAACGAA
Found at i:59091 original size:18 final size:18
Alignment explanation
Indices: 59065--59099 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
59055 CAACTCAACA
*
59065 GAGTGGAAGCTGAAGTTG
1 GAGTGGAAGCTCAAGTTG
*
59083 GAGTTGAAGCTCAAGTT
1 GAGTGGAAGCTCAAGTT
59100 TGGGACCTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.09, G:0.37, T:0.26
Consensus pattern (18 bp):
GAGTGGAAGCTCAAGTTG
Found at i:63656 original size:48 final size:48
Alignment explanation
Indices: 63593--63824 Score: 367
Period size: 48 Copynumber: 4.8 Consensus size: 48
63583 CAAACCCCCA
*
63593 CCAGACCACCCGGCGTTTAGAACAATTTCCAGAACAGCAACCAAACCC
1 CCAGACCACCCGGCGTTTAGAACAATCTCCAGAACAGCAACCAAACCC
*
63641 CCAGACCACCCGGCGTTTAGAGCAATCTCCAGAACAGCAACCAAACCC
1 CCAGACCACCCGGCGTTTAGAACAATCTCCAGAACAGCAACCAAACCC
* * *
63689 CCAGACCAGCCGGCGTTTAAAACAATCTCCAGAACAGCGACCAAACCC
1 CCAGACCACCCGGCGTTTAGAACAATCTCCAGAACAGCAACCAAACCC
* * * *
63737 CCAGACGACCTGGTGTTTAAAACAATCTCCAGAACAGCAACCAAACCC
1 CCAGACCACCCGGCGTTTAGAACAATCTCCAGAACAGCAACCAAACCC
63785 CCAGA-CAGCCCGGCGTTTAGAACAATCTCCAGAACAGCAA
1 CCAGACCA-CCCGGCGTTTAGAACAATCTCCAGAACAGCAA
63825 AGCTCCCGCC
Statistics
Matches: 168, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
47 1 0.01
48 167 0.99
ACGTcount: A:0.35, C:0.36, G:0.16, T:0.12
Consensus pattern (48 bp):
CCAGACCACCCGGCGTTTAGAACAATCTCCAGAACAGCAACCAAACCC
Found at i:75212 original size:3 final size:3
Alignment explanation
Indices: 75204--75228 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
75194 TTATCATTAA
75204 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
75229 GCTAGGAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:86943 original size:7 final size:7
Alignment explanation
Indices: 86931--86964 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
86921 ATTATTGGTG
86931 CTGCAAA
1 CTGCAAA
86938 CTGCAAA
1 CTGCAAA
86945 CTGCAAA
1 CTGCAAA
*
86952 CTGCAGA
1 CTGCAAA
86959 CTGCAA
1 CTGCAA
86965 TGCAATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.38, C:0.29, G:0.18, T:0.15
Consensus pattern (7 bp):
CTGCAAA
Found at i:87650 original size:30 final size:30
Alignment explanation
Indices: 87616--87673 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
87606 TATAATTTTT
87616 AATCATTAAAAGTTTATTTATTAATTATAG
1 AATCATTAAAAGTTTATTTATTAATTATAG
**
87646 AATCATTAAACTTTTATTTATTAATTAT
1 AATCATTAAAAGTTTATTTATTAATTAT
87674 GAAAAGATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.50
Consensus pattern (30 bp):
AATCATTAAAAGTTTATTTATTAATTATAG
Found at i:87830 original size:28 final size:28
Alignment explanation
Indices: 87798--87855 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
87788 AACAAATTAC
87798 AAACTAAACTCACATTCCGTGAGACTTG
1 AAACTAAACTCACATTCCGTGAGACTTG
*
87826 AAACTAAACTCACATTCTGTGAGACTTG
1 AAACTAAACTCACATTCCGTGAGACTTG
87854 AA
1 AA
87856 CCCAGGACCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (28 bp):
AAACTAAACTCACATTCCGTGAGACTTG
Found at i:88598 original size:58 final size:58
Alignment explanation
Indices: 88508--88624 Score: 225
Period size: 58 Copynumber: 2.0 Consensus size: 58
88498 GTAACTTACT
*
88508 TTCCACTGTTTGACCCATTACACGTGCACAATTTTTGTCATTCCAAAGGATTAGTTGG
1 TTCCACTGTTTGACCCATTACACGTGCACAATTTTTCTCATTCCAAAGGATTAGTTGG
88566 TTCCACTGTTTGACCCATTACACGTGCACAATTTTTCTCATTCCAAAGGATTAGTTGG
1 TTCCACTGTTTGACCCATTACACGTGCACAATTTTTCTCATTCCAAAGGATTAGTTGG
88624 T
1 T
88625 AAATGGTAAG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.37
Consensus pattern (58 bp):
TTCCACTGTTTGACCCATTACACGTGCACAATTTTTCTCATTCCAAAGGATTAGTTGG
Found at i:89778 original size:4 final size:4
Alignment explanation
Indices: 89769--89804 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
89759 ATGAATAGTT
*
89769 TTTA TTTA TTTA TTTA TTTA TCTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
89805 CAATCATCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:89976 original size:27 final size:28
Alignment explanation
Indices: 89938--89992 Score: 103
Period size: 27 Copynumber: 2.0 Consensus size: 28
89928 TTTCCTCAAA
89938 ACCTCATCAAGTGGTGCTGACAC-TTTT
1 ACCTCATCAAGTGGTGCTGACACGTTTT
89965 ACCTCATCAAGTGGTGCTGACACGTTTT
1 ACCTCATCAAGTGGTGCTGACACGTTTT
89993 TTCCACAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 23 0.85
28 4 0.15
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (28 bp):
ACCTCATCAAGTGGTGCTGACACGTTTT
Found at i:97395 original size:25 final size:25
Alignment explanation
Indices: 97367--97437 Score: 115
Period size: 25 Copynumber: 2.8 Consensus size: 25
97357 GCAGCCTATG
* *
97367 CGTTTGCTAAACACAAGCACAGACT
1 CGTTTGCCAAACGCAAGCACAGACT
*
97392 CGTTTGCCAAACGCAAGCACAGGCT
1 CGTTTGCCAAACGCAAGCACAGACT
97417 CGTTTGCCAAACGCAAGCACA
1 CGTTTGCCAAACGCAAGCACA
97438 TGAGCGTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.32, C:0.31, G:0.20, T:0.17
Consensus pattern (25 bp):
CGTTTGCCAAACGCAAGCACAGACT
Found at i:97445 original size:25 final size:24
Alignment explanation
Indices: 97366--97446 Score: 92
Period size: 25 Copynumber: 3.2 Consensus size: 24
97356 TGCAGCCTAT
* *
97366 GCGTTTGCTAAACACAAGCACAGA
1 GCGTTTGCCAAACGCAAGCACAGA
*
97390 CTCGTTTGCCAAACGCAAGCACAG-
1 -GCGTTTGCCAAACGCAAGCACAGA
97414 GCTCGTTTGCCAAACGCAAGCACATGA
1 G--CGTTTGCCAAACGCAAGCACA-GA
97441 GCGTTT
1 GCGTTT
97447 ACCCAGCGCA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
25 46 0.96
26 1 0.02
27 1 0.02
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.20
Consensus pattern (24 bp):
GCGTTTGCCAAACGCAAGCACAGA
Found at i:101703 original size:25 final size:25
Alignment explanation
Indices: 101599--101696 Score: 151
Period size: 25 Copynumber: 3.9 Consensus size: 25
101589 GCAGCCTATG
* *
101599 CGTTTGCTAAACGCAAGTACAGGCT
1 CGTTTGCTAAACGCAAGCACATGCT
*
101624 CGTTTGCTAAACGCAAGCACAAGCT
1 CGTTTGCTAAACGCAAGCACATGCT
101649 CGTTTGCTAAACGCAAGCACATGCT
1 CGTTTGCTAAACGCAAGCACATGCT
* *
101674 CGTTTGCCAAACGCAAGAACATG
1 CGTTTGCTAAACGCAAGCACATG
101697 AGCGTTTACC
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 68 1.00
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (25 bp):
CGTTTGCTAAACGCAAGCACATGCT
Found at i:106953 original size:27 final size:27
Alignment explanation
Indices: 106916--106976 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
106906 TGTTAGGTGG
106916 GAAA-TTGAACAGCAATCCTTAAATAT
1 GAAATTTGAACAGCAATCCTTAAATAT
106942 GAAATTTGAACAGCAATCCTTAAATAT
1 GAAATTTGAACAGCAATCCTTAAATAT
106969 GAAATTTG
1 GAAATTTG
106977 TAAAAGATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 4 0.12
27 30 0.88
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (27 bp):
GAAATTTGAACAGCAATCCTTAAATAT
Done.