Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015640.1 Corchorus capsularis cultivar CVL-1 contig15661, 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: 11459
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Found at i:146 original size:2 final size:2
Alignment explanation
Indices: 139--176 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
129 GAATTTCCTA
139 AT AT AT AT AT 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 AT AT AT AT AT
177 GTTCAATGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4082 original size:23 final size:24
Alignment explanation
Indices: 4054--4141 Score: 76
Period size: 25 Copynumber: 3.6 Consensus size: 24
4044 TTCTGTTTTC
4054 TAAATATA-AATATATTATTTATA
1 TAAATATATAATATATTATTTATA
*
4077 TAAATATATTAATAT-TTCTTATATA
1 TAAATATA-TAATATATTATT-TATA
*
4102 TATATATTATATAATATA-TA-ATATA
1 TA-A-A-TATATAATATATTATTTATA
*
4127 TATATATATAATATA
1 TAAATATATAATATA
4142 AAAAATTAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 15
0.74 0.05 0.21
Matches are distributed among these distances:
22 11 0.20
23 9 0.17
24 4 0.07
25 17 0.31
26 1 0.02
27 8 0.15
28 4 0.07
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (24 bp):
TAAATATATAATATATTATTTATA
Found at i:4120 original size:29 final size:27
Alignment explanation
Indices: 4056--4166 Score: 93
Period size: 27 Copynumber: 4.1 Consensus size: 27
4046 CTGTTTTCTA
* * *
4056 AATATAA-ATATATTATTTATATAAAT
1 AATATAATATATAATATATATATATAT
* **
4082 -ATATTAATATTTCTTATATATATATAT
1 AATA-TAATATATAATATATATATATAT
*
4109 TATATAATATATAATATATATATATAT
1 AATATAATATATAATATATATATATAT
* *
4136 AATATAAAAAATTAAT-TATTATATATAT
1 AATATAATATA-TAATATA-TATATATAT
4164 AAT
1 AAT
4167 CGGTTTGTCG
Statistics
Matches: 70, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
25 3 0.04
26 3 0.04
27 45 0.64
28 19 0.27
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (27 bp):
AATATAATATATAATATATATATATAT
Found at i:4161 original size:2 final size:2
Alignment explanation
Indices: 4057--4141 Score: 69
Period size: 2 Copynumber: 46.5 Consensus size: 2
4047 TGTTTTCTAA
* * * * *
4057 AT AT AA AT AT AT -T AT TT AT AT AA AT AT AT -T A- AT AT TT CT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4096 -T AT AT AT AT AT AT -T AT AT A- AT AT AT A- 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
4134 AT A- AT AT A
1 AT AT AT AT A
4142 AAAAATTAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 16
0.74 0.09 0.18
Matches are distributed among these distances:
1 8 0.12
2 59 0.88
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4714 original size:16 final size:16
Alignment explanation
Indices: 4695--4740 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
4685 TCGGTTAAGG
4695 GGGCTTTCGAAAATGA
1 GGGCTTTCGAAAATGA
* *
4711 GGGCTTTCAAAAATGG
1 GGGCTTTCGAAAATGA
4727 GGGCTTTCGAAAAT
1 GGGCTTTCGAAAAT
4741 AATAAATTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.30, C:0.13, G:0.30, T:0.26
Consensus pattern (16 bp):
GGGCTTTCGAAAATGA
Found at i:5451 original size:6 final size:6
Alignment explanation
Indices: 5440--5466 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5430 AAAGCAAAGC
5440 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
5467 GCAAAATAAT
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:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:5481 original size:13 final size:13
Alignment explanation
Indices: 5463--5497 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
5453 AATCTAAATC
5463 TAAAGCAAAATAA
1 TAAAGCAAAATAA
*
5476 TAAAGCAAATTAA
1 TAAAGCAAAATAA
5489 TAAAGCAAA
1 TAAAGCAAA
5498 CAATAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.66, C:0.09, G:0.09, T:0.17
Consensus pattern (13 bp):
TAAAGCAAAATAA
Found at i:5485 original size:12 final size:12
Alignment explanation
Indices: 5463--5503 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
5453 AATCTAAATC
5463 TAAAGCAAAATAA
1 TAAAGC-AAATAA
5476 TAAAGCAAATTAA
1 TAAAGCAAA-TAA
*
5489 TAAAGCAAACAA
1 TAAAGCAAATAA
5501 TAA
1 TAA
5504 TTATAAAGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 8 0.31
13 18 0.69
ACGTcount: A:0.66, C:0.10, G:0.07, T:0.17
Consensus pattern (12 bp):
TAAAGCAAATAA
Found at i:6443 original size:10 final size:10
Alignment explanation
Indices: 6428--6452 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
6418 GAGGACTCTA
6428 GAATTTTCTG
1 GAATTTTCTG
6438 GAATTTTCTG
1 GAATTTTCTG
6448 GAATT
1 GAATT
6453 GAACGGGGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:7209 original size:29 final size:29
Alignment explanation
Indices: 7167--7235 Score: 129
Period size: 29 Copynumber: 2.4 Consensus size: 29
7157 TAAAGTGGCA
*
7167 TCAAAATAAAACTTCCGGGTATATTTTGG
1 TCAAAATAAAACTTCCGGGTACATTTTGG
7196 TCAAAATAAAACTTCCGGGTACATTTTGG
1 TCAAAATAAAACTTCCGGGTACATTTTGG
7225 TCAAAATAAAA
1 TCAAAATAAAA
7236 AAGTTGGGGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (29 bp):
TCAAAATAAAACTTCCGGGTACATTTTGG
Found at i:11243 original size:33 final size:33
Alignment explanation
Indices: 11195--11285 Score: 103
Period size: 33 Copynumber: 2.7 Consensus size: 33
11185 CCGCGCAACA
*
11195 CCGGCCACAAGACCGGCCACGCGACAT-GGACATGT
1 CCGGCCAC-A-ACCGGCCACGCGAC-TCGGACATGC
* ** *
11230 CCGGCTACAACCGGCCAAACGACTCGGCCATGC
1 CCGGCCACAACCGGCCACGCGACTCGGACATGC
11263 CCGGCCACAACCGGCCACGCGAC
1 CCGGCCACAACCGGCCACGCGAC
11286 CCTTTGTCTA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
32 1 0.02
33 38 0.81
34 1 0.02
35 7 0.15
ACGTcount: A:0.24, C:0.43, G:0.26, T:0.07
Consensus pattern (33 bp):
CCGGCCACAACCGGCCACGCGACTCGGACATGC
Done.