Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008417.1 Corchorus capsularis cultivar CVL-1 contig08438, 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: 38945
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1803 original size:33 final size:33
Alignment explanation
Indices: 1766--1839 Score: 114
Period size: 33 Copynumber: 2.2 Consensus size: 33
1756 CGGCCACAAG
**
1766 ACCGGCCACGCGACATGGACATGTCCGGCTATC-
1 ACCGGCCACGCGACATGGACATAACCGGCTA-CA
1799 ACCGGCCACGCGACATGGACATAACCGGCTACA
1 ACCGGCCACGCGACATGGACATAACCGGCTACA
1832 ACCGGCCA
1 ACCGGCCA
1840 ATCGACTCGG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 1 0.03
33 37 0.97
ACGTcount: A:0.26, C:0.38, G:0.26, T:0.11
Consensus pattern (33 bp):
ACCGGCCACGCGACATGGACATAACCGGCTACA
Found at i:2832 original size:98 final size:98
Alignment explanation
Indices: 2663--2861 Score: 380
Period size: 98 Copynumber: 2.0 Consensus size: 98
2653 TATCACTTGA
2663 ACCTGAGATCTTTTTTTAAAGACCATAGAACTTCTTCCATTTGAGATAAGAATCATTTTCATTTC
1 ACCTGAGATCTTTTTTTAAAGACCATAGAACTTCTTCCATTTGAGATAAGAATCATTTTCATTTC
* *
2728 TTGAAGAGATTGTGATTACAAACACACAGGAAG
66 TTGAAGAAATTGGGATTACAAACACACAGGAAG
2761 ACCTGAGATCTTTTTTTAAAGACCATAGAACTTCTTCCATTTGAGATAAGAATCATTTTCATTTC
1 ACCTGAGATCTTTTTTTAAAGACCATAGAACTTCTTCCATTTGAGATAAGAATCATTTTCATTTC
2826 TTGAAGAAATTGGGATTACAAACACACAGGAAG
66 TTGAAGAAATTGGGATTACAAACACACAGGAAG
2859 ACC
1 ACC
2862 CGTACACCGC
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 99 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (98 bp):
ACCTGAGATCTTTTTTTAAAGACCATAGAACTTCTTCCATTTGAGATAAGAATCATTTTCATTTC
TTGAAGAAATTGGGATTACAAACACACAGGAAG
Found at i:3654 original size:30 final size:30
Alignment explanation
Indices: 3618--3685 Score: 136
Period size: 30 Copynumber: 2.3 Consensus size: 30
3608 CTCGAAGCTC
3618 GGCTCGAGTTCGGCCGAGCCTCATTTTGGA
1 GGCTCGAGTTCGGCCGAGCCTCATTTTGGA
3648 GGCTCGAGTTCGGCCGAGCCTCATTTTGGA
1 GGCTCGAGTTCGGCCGAGCCTCATTTTGGA
3678 GGCTCGAG
1 GGCTCGAG
3686 CTCGACTCGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.13, C:0.26, G:0.35, T:0.25
Consensus pattern (30 bp):
GGCTCGAGTTCGGCCGAGCCTCATTTTGGA
Found at i:6599 original size:7 final size:7
Alignment explanation
Indices: 6589--6623 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
6579 TTCTTTACCT
6589 TTTAGGG
1 TTTAGGG
6596 TTTAGGG
1 TTTAGGG
6603 TTTAGGG
1 TTTAGGG
6610 -TTAGGG
1 TTTAGGG
6616 TTTAGGG
1 TTTAGGG
6623 T
1 T
6624 AAAACCTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43
Consensus pattern (7 bp):
TTTAGGG
Found at i:6615 original size:13 final size:13
Alignment explanation
Indices: 6589--6623 Score: 61
Period size: 13 Copynumber: 2.6 Consensus size: 13
6579 TTCTTTACCT
6589 TTTAGGGTTTAGGG
1 TTTAGGG-TTAGGG
6603 TTTAGGGTTAGGG
1 TTTAGGGTTAGGG
6616 TTTAGGGT
1 TTTAGGGT
6624 AAAACCTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.67
14 7 0.33
ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43
Consensus pattern (13 bp):
TTTAGGGTTAGGG
Found at i:11525 original size:23 final size:23
Alignment explanation
Indices: 11499--11545 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
11489 GAAGATAAAG
11499 AAGTCG-ATAAGGCAAGGCAGCCC
1 AAGTCGAATAA-GCAAGGCAGCCC
*
11522 AAGTCGACATAAGCATGGCAGCCC
1 AAGTCGA-ATAAGCAAGGCAGCCC
11546 CAAGGGGCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 6 0.29
24 11 0.52
25 4 0.19
ACGTcount: A:0.34, C:0.28, G:0.28, T:0.11
Consensus pattern (23 bp):
AAGTCGAATAAGCAAGGCAGCCC
Found at i:16078 original size:2 final size:2
Alignment explanation
Indices: 16073--16103 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
16063 AGTGTGTGTG
16073 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16104 TGGTATAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16570 original size:14 final size:14
Alignment explanation
Indices: 16551--16590 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
16541 GAGAGGACAT
*
16551 GGAGAGGGGAGAGG
1 GGAGAGGAGAGAGG
16565 GGAGAGGAGAGAGG
1 GGAGAGGAGAGAGG
*
16579 AGGTGAGGAGAG
1 -GGAGAGGAGAG
16591 GGCATGGTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.33, C:0.00, G:0.65, T:0.03
Consensus pattern (14 bp):
GGAGAGGAGAGAGG
Found at i:17546 original size:22 final size:24
Alignment explanation
Indices: 17522--17568 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
17512 CTAAATAAAA
17522 AAGAAGAGAGGAAAAAAACGCAAAG
1 AAGAAGAGA-GAAAAAAACGCAAAG
* *
17547 AAGAAGAGAGAATAAAAGGCAA
1 AAGAAGAGAGAAAAAAACGCAA
17569 TTTCTCCGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.64, C:0.06, G:0.28, T:0.02
Consensus pattern (24 bp):
AAGAAGAGAGAAAAAAACGCAAAG
Found at i:23666 original size:17 final size:18
Alignment explanation
Indices: 23652--23685 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
23642 CACTAGTGTT
23652 CTAAGATCACCAGTGATG
1 CTAAGATCACCAGTGATG
*
23670 C-AAGATCACCGGTGAT
1 CTAAGATCACCAGTGAT
23686 CAAAGATTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 14 0.93
18 1 0.07
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.21
Consensus pattern (18 bp):
CTAAGATCACCAGTGATG
Found at i:24990 original size:31 final size:31
Alignment explanation
Indices: 24872--24979 Score: 146
Period size: 31 Copynumber: 3.5 Consensus size: 31
24862 GTGTCCAACA
* *
24872 TGGCACGCCA-AGTGTACCAAAAAATGACATG
1 TGGCACGCCACA-TGTACCAAAAAGTGACACG
*
24903 TGGCACGCCACATGTACCAAAAAGTGACACA
1 TGGCACGCCACATGTACCAAAAAGTGACACG
* *
24934 TGTCACGCCACGTGTACCAAAAAGTGACACG
1 TGGCACGCCACATGTACCAAAAAGTGACACG
*
24965 TGGCATGCCACATGT
1 TGGCACGCCACATGT
24980 TTCGAAAAGT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
31 66 0.99
32 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.22, T:0.17
Consensus pattern (31 bp):
TGGCACGCCACATGTACCAAAAAGTGACACG
Found at i:25500 original size:15 final size:15
Alignment explanation
Indices: 25480--25544 Score: 67
Period size: 15 Copynumber: 4.2 Consensus size: 15
25470 CCCGAACCTG
*
25480 GAAAAATCCGAATCC
1 GAAAAATCCGAACCC
* *
25495 GAAAAAACTCAAACCC
1 GAAAAATC-CGAACCC
*
25511 GAAAAAATCAGAACCC
1 G-AAAAATCCGAACCC
*
25527 GAAAAACCCGAACCC
1 GAAAAATCCGAACCC
25542 GAA
1 GAA
25545 TCCAAAATGT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
15 22 0.55
16 12 0.30
17 6 0.15
ACGTcount: A:0.52, C:0.29, G:0.12, T:0.06
Consensus pattern (15 bp):
GAAAAATCCGAACCC
Found at i:25500 original size:16 final size:16
Alignment explanation
Indices: 25471--25544 Score: 71
Period size: 16 Copynumber: 4.7 Consensus size: 16
25461 CTGTCCGAAC
* *
25471 CCGAACCTGGAAAAAT
1 CCGAACCCGAAAAAAT
*
25487 CCGAATCCGAAAAAA-
1 CCGAACCCGAAAAAAT
*
25502 CTCAAACCCGAAAAAAT
1 C-CGAACCCGAAAAAAT
* *
25519 CAGAACCCG-AAAAAC
1 CCGAACCCGAAAAAAT
25534 CCGAACCCGAA
1 CCGAACCCGAA
25545 TCCAAAATGT
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
15 14 0.30
16 31 0.67
17 1 0.02
ACGTcount: A:0.49, C:0.31, G:0.14, T:0.07
Consensus pattern (16 bp):
CCGAACCCGAAAAAAT
Found at i:28571 original size:24 final size:24
Alignment explanation
Indices: 28539--28585 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
28529 AATGGCTTTG
28539 TGGTTTATATAAAGTGATGATATA
1 TGGTTTATATAAAGTGATGATATA
*
28563 TGGTTTATATAAATTGATGATAT
1 TGGTTTATATAAAGTGATGATAT
28586 GAAAGATTAA
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:0.36, C:0.00, G:0.19, T:0.45
Consensus pattern (24 bp):
TGGTTTATATAAAGTGATGATATA
Found at i:31673 original size:33 final size:33
Alignment explanation
Indices: 31636--31731 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 33
31626 GGCGGCTGAG
31636 CCATGGCCAAGCCGCCCTCCTGGGGCGGCAATA
1 CCATGGCCAAGCCGCCCTCCTGGGGCGGCAATA
* **
31669 CCATGGCCAGGCCG-CCTCCCTGGGGCGGCCCTA
1 CCATGGCCAAGCCGCCCT-CCTGGGGCGGCAATA
*
31702 CCATGG--ATAGACCGCCCCCCTGGGGCGGCA
1 CCATGGCCA-AG-CCGCCCTCCTGGGGCGGCA
31732 CCGGTACTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
31 1 0.02
32 4 0.08
33 46 0.87
34 2 0.04
ACGTcount: A:0.15, C:0.42, G:0.32, T:0.11
Consensus pattern (33 bp):
CCATGGCCAAGCCGCCCTCCTGGGGCGGCAATA
Found at i:31822 original size:32 final size:32
Alignment explanation
Indices: 31771--31941 Score: 235
Period size: 32 Copynumber: 5.4 Consensus size: 32
31761 AAAAAGCCTT
* *
31771 GCCGCCCTAGTGGGGCGGCTAGCCGTGGCAGA
1 GCCGTCCTAGTGGGACGGCTAGCCGTGGCAGA
31803 GCCGTCCTAGTGGGACGGCTAGCCGTGGCAGA
1 GCCGTCCTAGTGGGACGGCTAGCCGTGGCAGA
*
31835 GCCGTCCTAGTGGGGCGGCTAGCCGTGGCAGA
1 GCCGTCCTAGTGGGACGGCTAGCCGTGGCAGA
*
31867 GCCGTCCTAGT-GG--GGC-GGCCGTGGCAGA
1 GCCGTCCTAGTGGGACGGCTAGCCGTGGCAGA
* *
31895 GCCGTCCTAGTGGGGA-GGCTCCGCCGTGGTAGA
1 GCCGTCCTAGT-GGGACGGCT-AGCCGTGGCAGA
31928 GCCGTCCTAGTGGG
1 GCCGTCCTAGTGGG
31942 GAGACTTCGC
Statistics
Matches: 128, Mismatches: 6, Indels: 10
0.89 0.04 0.07
Matches are distributed among these distances:
28 22 0.17
29 3 0.02
30 2 0.02
31 5 0.04
32 75 0.59
33 21 0.16
ACGTcount: A:0.12, C:0.29, G:0.43, T:0.16
Consensus pattern (32 bp):
GCCGTCCTAGTGGGACGGCTAGCCGTGGCAGA
Found at i:35085 original size:6 final size:6
Alignment explanation
Indices: 35074--35121 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
35064 CCTACGTCCT
* * * *
35074 ACCAAA ACCAAA ACCAAA AACAAA AGCAAA AACAAA AACAAA ATCCAA
1 ACCAAA ACCAAA ACCAAA ACCAAA ACCAAA ACCAAA ACCAAA A-CCAA
35122 TTCCCTTCCA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
6 34 0.92
7 3 0.08
ACGTcount: A:0.71, C:0.25, G:0.02, T:0.02
Consensus pattern (6 bp):
ACCAAA
Found at i:35091 original size:12 final size:12
Alignment explanation
Indices: 35074--35116 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
35064 CCTACGTCCT
*
35074 ACCAAAACCAAA
1 ACCAAAAACAAA
35086 ACCAAAAACAAA
1 ACCAAAAACAAA
*
35098 AGCAAAAACAAA
1 ACCAAAAACAAA
*
35110 AACAAAA
1 ACCAAAA
35117 TCCAATTCCC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.74, C:0.23, G:0.02, T:0.00
Consensus pattern (12 bp):
ACCAAAAACAAA
Found at i:35103 original size:18 final size:18
Alignment explanation
Indices: 35076--35121 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
35066 TACGTCCTAC
*
35076 CAAAACCAAAACCAAAAA
1 CAAAACCAAAAACAAAAA
*
35094 CAAAAGCAAAAACAAAAA
1 CAAAACCAAAAACAAAAA
35112 CAAAATCCAA
1 CAAAA-CCAA
35122 TTCCCTTCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 21 0.88
19 3 0.12
ACGTcount: A:0.72, C:0.24, G:0.02, T:0.02
Consensus pattern (18 bp):
CAAAACCAAAAACAAAAA
Done.