Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011137.1 Corchorus capsularis cultivar CVL-1 contig11158, 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: 84669
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:614 original size:27 final size:31
Alignment explanation
Indices: 567--634 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 31
557 CGAAGACTAG
567 TATATATAAA-TATATGTTATTA-TAT-TT-
1 TATATATAAATTATATGTTATTATTATATTA
*
594 T-TATATAAATTTTATGTTATTATTATATTA
1 TATATATAAATTATATGTTATTATTATATTA
624 TATATATAAAT
1 TATATATAAAT
635 ATAATAACAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
26 8 0.23
27 12 0.34
28 3 0.09
29 2 0.06
30 1 0.03
31 9 0.26
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (31 bp):
TATATATAAATTATATGTTATTATTATATTA
Found at i:9120 original size:30 final size:30
Alignment explanation
Indices: 9079--9141 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
9069 CACTGAACAC
9079 TGAATTCGGGTATTCACACTAGTCCAGATT
1 TGAATTCGGGTATTCACACTAGTCCAGATT
*
9109 TGAATTTGGGTATTCACACTAGTCCAGATT
1 TGAATTCGGGTATTCACACTAGTCCAGATT
9139 TGA
1 TGA
9142 GTCCCTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (30 bp):
TGAATTCGGGTATTCACACTAGTCCAGATT
Found at i:22295 original size:1 final size:1
Alignment explanation
Indices: 22289--22313 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
22279 TGACTTATTC
22289 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
22314 AACTTTCCAA
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:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:23695 original size:2 final size:2
Alignment explanation
Indices: 23688--23713 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
23678 ATCACAATTA
23688 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
23714 CAACATCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39155 original size:12 final size:12
Alignment explanation
Indices: 39118--39159 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
39108 CTGACCGTTT
39118 TGTTGCGGCTGC
1 TGTTGCGGCTGC
* *
39130 TGCTGCTGCTGC
1 TGTTGCGGCTGC
*
39142 TGTTGCGGCGGC
1 TGTTGCGGCTGC
39154 TGTTGC
1 TGTTGC
39160 TTAGAGTTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.00, C:0.26, G:0.40, T:0.33
Consensus pattern (12 bp):
TGTTGCGGCTGC
Found at i:46503 original size:2 final size:2
Alignment explanation
Indices: 46498--46527 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
46488 AAAAAGGGGA
46498 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
46528 ATAATAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56015 original size:13 final size:13
Alignment explanation
Indices: 55997--56023 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
55987 GATTTTTATC
55997 TTATTTTCTTCTA
1 TTATTTTCTTCTA
56010 TTATTTTCTTCTA
1 TTATTTTCTTCTA
56023 T
1 T
56024 CAATGTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (13 bp):
TTATTTTCTTCTA
Found at i:62906 original size:14 final size:14
Alignment explanation
Indices: 62889--62915 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
62879 ATGTTGATCC
62889 GGAAGTTGTGATTA
1 GGAAGTTGTGATTA
62903 GGAAGTTGTGATT
1 GGAAGTTGTGATT
62916 TGTGATGAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.37, T:0.37
Consensus pattern (14 bp):
GGAAGTTGTGATTA
Found at i:63031 original size:16 final size:16
Alignment explanation
Indices: 62996--63031 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
62986 GCTTCCTTTA
* *
62996 TTTCTTTTTTTTTTTT
1 TTTCTTTTTTTTTATC
63012 TTTCTTTTTTTTTATC
1 TTTCTTTTTTTTTATC
63028 TTTC
1 TTTC
63032 ATTGTGCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (16 bp):
TTTCTTTTTTTTTATC
Found at i:71676 original size:25 final size:25
Alignment explanation
Indices: 71629--71677 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
71619 TTAGTAGAAT
**
71629 AATTGTAAAAGTTTATTTCTAAAAA
1 AATTGTAAAAGAATATTTCTAAAAA
71654 AATTGTAAAAGAATATATT-TAAAA
1 AATTGTAAAAGAATAT-TTCTAAAA
71678 TTTTTTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (25 bp):
AATTGTAAAAGAATATTTCTAAAAA
Found at i:72144 original size:23 final size:23
Alignment explanation
Indices: 72087--72145 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 23
72077 TAAAATAATT
72087 ATAAAATATTGAATTTTTTGAGATA
1 ATAAAATATTGAATTTTTT--GATA
72112 ATAAAATATTGAATTTATTT-A-A
1 ATAAAATATTGAATTT-TTTGATA
72134 ATGAAAATATTG
1 AT-AAAATATTG
72146 TTTTTAGTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
22 3 0.09
23 10 0.31
25 16 0.50
26 3 0.09
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.42
Consensus pattern (23 bp):
ATAAAATATTGAATTTTTTGATA
Found at i:76285 original size:2 final size:2
Alignment explanation
Indices: 76278--76308 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
76268 TTGTTTGTTC
76278 AT 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 AT A
76309 ATTCCGTAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:81757 original size:6 final size:6
Alignment explanation
Indices: 81746--81772 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
81736 ATAAATTTTG
81746 TCAGCT TCAGCT TCAGCT TCAGCT TCA
1 TCAGCT TCAGCT TCAGCT TCAGCT TCA
81773 TACCTGTGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.33, G:0.15, T:0.33
Consensus pattern (6 bp):
TCAGCT
Found at i:84210 original size:2 final size:2
Alignment explanation
Indices: 84190--84231 Score: 59
Period size: 2 Copynumber: 21.0 Consensus size: 2
84180 GCACATGATC
*
84190 AT AT CAT AT AT TT AT -T 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 AT AT AT AT AT
84232 TGAAACCTCG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.92
3 2 0.06
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Done.