Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006769.1 Corchorus capsularis cultivar CVL-1 contig06790, 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: 43254
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:4927 original size:41 final size:41
Alignment explanation
Indices: 4882--4964 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
4872 TCAAGTGATT
*
4882 GATTCGACGCACAAATCTCTTTCTTGGCACCCAAAAGAAAA
1 GATTCGACGCACAAATATCTTTCTTGGCACCCAAAAGAAAA
4923 GATTCGACGCACAAATATCTTTCTTGGCACCCAAAAGAAAA
1 GATTCGACGCACAAATATCTTTCTTGGCACCCAAAAGAAAA
4964 G
1 G
4965 GATTACCACG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.22
Consensus pattern (41 bp):
GATTCGACGCACAAATATCTTTCTTGGCACCCAAAAGAAAA
Found at i:6281 original size:28 final size:30
Alignment explanation
Indices: 6241--6316 Score: 97
Period size: 28 Copynumber: 2.6 Consensus size: 30
6231 TTCTTTTTTT
6241 AAACTTAAGGGATTAATTT-GT-CCAAA-AA
1 AAACTTAAGGGATT-ATTTCGTCCCAAACAA
*
6269 AAACATAAGGGATTATTTCGTCCCAAACGAA
1 AAACTTAAGGGATTATTTCGTCCCAAAC-AA
6300 AAACTTAAGGGA-TATTT
1 AAACTTAAGGGATTATTT
6317 TTGGGTATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 4 0.10
28 15 0.36
29 5 0.12
30 5 0.12
31 13 0.31
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (30 bp):
AAACTTAAGGGATTATTTCGTCCCAAACAA
Found at i:6557 original size:87 final size:88
Alignment explanation
Indices: 6370--6557 Score: 238
Period size: 87 Copynumber: 2.1 Consensus size: 88
6360 ATTATTTAGC
*
6370 CCCATTACTAGTAGCAATTTGCCTAATCATGCTTTACAGTATCACCATACATGATTTGGGGTTTA
1 CCCATTACTAGTAGCAATTTGCCTAATCATGCTTTACAATATCACCATACATGATTTGGGGTTTA
* *
6435 ACTATTACGTTTTGCGGTTTGAT
66 ACCATTACGATTTGCGGTTTGAT
* *** * *
6458 CCCATTATTAGTAGGGGTTTGCCTAATCATGCTTT-CAA-ATTCACTATACATGATTTGGGTTTT
1 CCCATTACTAGTAGCAATTTGCCTAATCATGCTTTACAATA-TCACCATACATGATTTGGGGTTT
* *
6521 GACCATTATGATTTG-GGATTTGAT
65 AACCATTACGATTTGCGG-TTTGAT
6545 CCCATTACTAGTA
1 CCCATTACTAGTA
6558 AGAGTTTAAA
Statistics
Matches: 86, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
86 3 0.03
87 52 0.60
88 31 0.36
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (88 bp):
CCCATTACTAGTAGCAATTTGCCTAATCATGCTTTACAATATCACCATACATGATTTGGGGTTTA
ACCATTACGATTTGCGGTTTGAT
Found at i:6635 original size:2 final size:2
Alignment explanation
Indices: 6628--6655 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6618 TGGATAAATC
6628 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
6656 GTTCATTAAG
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:6893 original size:22 final size:21
Alignment explanation
Indices: 6824--6898 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
6814 TGACTTTCAT
6824 ATTTGGGGTTTGACCATTAAG
1 ATTTGGGGTTTGACCATTAAG
* * ** * *
6845 ATTTCGGGTTTCATAATCGATG
1 ATTTGGGGTTTGACCAT-TAAG
6867 A-TTGGGGCTTTGACCATTAAG
1 ATTTGGGG-TTTGACCATTAAG
6888 ATTTGGGGTTT
1 ATTTGGGGTTT
6899 AATCCCATTA
Statistics
Matches: 39, Mismatches: 12, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
21 24 0.62
22 15 0.38
ACGTcount: A:0.21, C:0.11, G:0.28, T:0.40
Consensus pattern (21 bp):
ATTTGGGGTTTGACCATTAAG
Found at i:7108 original size:88 final size:88
Alignment explanation
Indices: 6879--7113 Score: 228
Period size: 88 Copynumber: 2.7 Consensus size: 88
6869 TGGGGCTTTG
* * * * *
6879 ACCATTAAGATTTGGGGTTTAATCCCATTAC-A-TCCCTGGGATTGCCTAATCATGCTTTACAAT
1 ACCATTACGATTTGCGGTTTGATCCCATTACTAGT-AC-GGGTTTGCCTAATCATGCTTTACAAT
*
6942 TTCACCATACATGATTTAGAGTTTG
64 TTCACCATACATGATTTAGAGTTTA
* * * * ** *
6967 ATCATTACGCTTTGCGGTTTGATCCCATTATTAGTAGGGGTTTAG-GGAATCATGCTTTACAGTT
1 ACCATTACGATTTGCGGTTTGATCCCATTACTAGTACGGGTTT-GCCTAATCATGCTTTACAATT
* *
7031 TCACCGTACATGATTT-GGGATTTA
65 TCACCATACATGATTTAGAG-TTTA
* * *
7055 ACCATTACGATTTG-GGCTTTGATTCCATTACTAGTACTGGTTTGCCTATTCATGCTTTA
1 ACCATTACGATTTGCGG-TTTGATCCCATTACTAGTACGGGTTTGCCTAATCATGCTTTA
7114 TATTTGGTGG
Statistics
Matches: 117, Mismatches: 24, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
87 5 0.04
88 109 0.93
89 2 0.02
90 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.39
Consensus pattern (88 bp):
ACCATTACGATTTGCGGTTTGATCCCATTACTAGTACGGGTTTGCCTAATCATGCTTTACAATTT
CACCATACATGATTTAGAGTTTA
Found at i:13386 original size:13 final size:13
Alignment explanation
Indices: 13346--13389 Score: 51
Period size: 11 Copynumber: 3.6 Consensus size: 13
13336 TCACAATATT
13346 CAATTAAAACAAA
1 CAATTAAAACAAA
13359 C--TCTAAAA-AAA
1 CAAT-TAAAACAAA
13370 -AATTAAAACAAA
1 CAATTAAAACAAA
13382 CAATTAAA
1 CAATTAAA
13390 TAATAATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
11 9 0.35
12 9 0.35
13 8 0.31
ACGTcount: A:0.68, C:0.14, G:0.00, T:0.18
Consensus pattern (13 bp):
CAATTAAAACAAA
Found at i:14836 original size:38 final size:36
Alignment explanation
Indices: 14781--14888 Score: 132
Period size: 34 Copynumber: 3.0 Consensus size: 36
14771 AATCAAATTA
*
14781 AATTTTTTTAGTCCAATTCCAATTATATATTACGAGTTG
1 AATTTTATTAGTCCAATTCCAATTATATATTACG-G--G
*
14820 AATTTTATTAG-CCAATTCAAATTATATATTACGGG
1 AATTTTATTAGTCCAATTCCAATTATATATTACGGG
* *
14855 --TTTTCTTAGTCCAATTCCAATTACATATTACGGG
1 AATTTTATTAGTCCAATTCCAATTATATATTACGGG
14889 TTAAGTGGAT
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
33 8 0.13
34 22 0.35
35 1 0.02
37 1 0.02
38 21 0.33
39 10 0.16
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (36 bp):
AATTTTATTAGTCCAATTCCAATTATATATTACGGG
Found at i:23689 original size:27 final size:27
Alignment explanation
Indices: 23658--23721 Score: 110
Period size: 27 Copynumber: 2.3 Consensus size: 27
23648 ATTTCTGGAA
*
23658 AACAAGGGAAAGGGACAATTAAAAAGG
1 AACAAGGGAAAGAGACAATTAAAAAGG
23685 AACAAGGGAAAGAGACAATTAAAAAGG
1 AACAAGGGAAAGAGACAATTAAAAAGG
23712 AACAGAGGGA
1 AACA-AGGGA
23722 GTAGTATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 30 0.86
28 5 0.14
ACGTcount: A:0.56, C:0.08, G:0.30, T:0.06
Consensus pattern (27 bp):
AACAAGGGAAAGAGACAATTAAAAAGG
Found at i:28319 original size:27 final size:27
Alignment explanation
Indices: 28286--28340 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
28276 TATATAATAT
*
28286 ATATATATAAACAAAATTTGTTAGAGA
1 ATATATATAAACAAAAATTGTTAGAGA
28313 ATATATATAAACAAAAATTGTTAGAGA
1 ATATATATAAACAAAAATTGTTAGAGA
28340 A
1 A
28341 GCAACAGCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.55, C:0.04, G:0.11, T:0.31
Consensus pattern (27 bp):
ATATATATAAACAAAAATTGTTAGAGA
Found at i:28631 original size:2 final size:2
Alignment explanation
Indices: 28619--28650 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
28609 ACCAAGATAC
28619 AT AT AT GAT 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 AT A
28651 ACATTCATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:29556 original size:2 final size:2
Alignment explanation
Indices: 29549--29578 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
29539 TAGGAAAGGG
29549 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
29579 ATCTGAGTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:31453 original size:6 final size:7
Alignment explanation
Indices: 31438--31462 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
31428 TTTTGTTTTG
31438 TTTTATT
1 TTTTATT
31445 TTTTATT
1 TTTTATT
31452 TTTTATT
1 TTTTATT
31459 TTTT
1 TTTT
31463 GGCAAGAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTATT
Found at i:33656 original size:3 final size:3
Alignment explanation
Indices: 33648--33693 Score: 74
Period size: 3 Copynumber: 14.7 Consensus size: 3
33638 TACTTCGATG
33648 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT ATAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT -TAT TA
33694 GAAGTGAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 35 0.83
4 7 0.17
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:34852 original size:16 final size:16
Alignment explanation
Indices: 34827--34860 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
34817 AATATAGGCC
* *
34827 ATAAACTTGGTAGAAG
1 ATAAAATTGGAAGAAG
34843 ATAAAATTGGAAGAAG
1 ATAAAATTGGAAGAAG
34859 AT
1 AT
34861 TGGATAACAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.24, T:0.24
Consensus pattern (16 bp):
ATAAAATTGGAAGAAG
Found at i:37795 original size:1 final size:1
Alignment explanation
Indices: 37789--37813 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
37779 ATATATTAGA
37789 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
37814 AAAGATGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Done.