Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015311.1 Corchorus capsularis cultivar CVL-1 contig15332, 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: 51728
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:896 original size:2 final size:2
Alignment explanation
Indices: 889--913 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
879 TGAGCTTTAC
889 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 A
914 GATAACAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10258 original size:15 final size:18
Alignment explanation
Indices: 10238--10278 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 18
10228 CAATATTCAA
10238 TTCTTCT-TCT-TC-TTC
1 TTCTTCTCTCTCTCTTTC
10253 TTCTTCTCTCTCTCTTTC
1 TTCTTCTCTCTCTCTTTC
10271 TTCCTTCT
1 TT-CTTCT
10279 GGGTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 7 0.32
16 3 0.14
17 2 0.09
18 5 0.23
19 5 0.23
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (18 bp):
TTCTTCTCTCTCTCTTTC
Found at i:12155 original size:14 final size:15
Alignment explanation
Indices: 12136--12175 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
12126 CCTGTAGTTG
12136 GAAAAAGAAAGAA-A
1 GAAAAAGAAAGAAGA
*
12150 GAAAAAGCAAGAAGA
1 GAAAAAGAAAGAAGA
*
12165 GAAAAAAAAAG
1 GAAAAAGAAAG
12176 GGTTCTATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.75, C:0.03, G:0.23, T:0.00
Consensus pattern (15 bp):
GAAAAAGAAAGAAGA
Found at i:12173 original size:19 final size:18
Alignment explanation
Indices: 12140--12175 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
12130 TAGTTGGAAA
*
12140 AAGAAAGAAAGAAAAAGC
1 AAGAAAGAAAAAAAAAGC
12158 AAGAAGAGAAAAAAAAAG
1 AAGAA-AGAAAAAAAAAG
12176 GGTTCTATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.75, C:0.03, G:0.22, T:0.00
Consensus pattern (18 bp):
AAGAAAGAAAAAAAAAGC
Found at i:13031 original size:3 final size:3
Alignment explanation
Indices: 12974--13016 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
12964 GGAAAAGAGG
12974 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
13017 GGAAAATTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:13055 original size:2 final size:2
Alignment explanation
Indices: 13048--13073 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13038 ATTTTGTGAC
13048 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
13074 TTTTAAAACT
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:14629 original size:103 final size:103
Alignment explanation
Indices: 14450--14660 Score: 422
Period size: 103 Copynumber: 2.0 Consensus size: 103
14440 GACTAGTTCT
14450 CCTAGTCATAATAGGAACTAAATACCCTATGTTTATATTTAACATAAAAACATTATTTTTTATAA
1 CCTAGTCATAATAGGAACTAAATACCCTATGTTTATATTTAACATAAAAACATTATTTTTTATAA
14515 TAAATATATTAAAAAGTGCATGAGCCATGGTATGCCGC
66 TAAATATATTAAAAAGTGCATGAGCCATGGTATGCCGC
14553 CCTAGTCATAATAGGAACTAAATACCCTATGTTTATATTTAACATAAAAACATTATTTTTTATAA
1 CCTAGTCATAATAGGAACTAAATACCCTATGTTTATATTTAACATAAAAACATTATTTTTTATAA
14618 TAAATATATTAAAAAGTGCATGAGCCATGGTATGCCGC
66 TAAATATATTAAAAAGTGCATGAGCCATGGTATGCCGC
14656 CCTAG
1 CCTAG
14661 GGCGGTTAAG
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (103 bp):
CCTAGTCATAATAGGAACTAAATACCCTATGTTTATATTTAACATAAAAACATTATTTTTTATAA
TAAATATATTAAAAAGTGCATGAGCCATGGTATGCCGC
Found at i:14722 original size:33 final size:32
Alignment explanation
Indices: 14635--14732 Score: 103
Period size: 33 Copynumber: 3.1 Consensus size: 32
14625 ATTAAAAAGT
*
14635 GCATGAGCCATGGTATGCCG-C-CCTAGGGCG
1 GCATGAGCCATGGTATGCCGCCTCCTGGGGCG
* * * * *
14665 G-TTAAGCCACGGCATGCCGCCCTCCTGGGGTG
1 GCATGAGCCATGGTATGCCG-CCTCCTGGGGCG
14697 GCATGAGCCATGGTATGCCGTCCTCCTGGGGCG
1 GCATGAGCCATGGTATGCCG-CCTCCTGGGGCG
14730 GCA
1 GCA
14733 AATACCAAGG
Statistics
Matches: 52, Mismatches: 12, Indels: 5
0.75 0.17 0.07
Matches are distributed among these distances:
29 14 0.27
30 1 0.02
31 1 0.02
32 8 0.15
33 28 0.54
ACGTcount: A:0.14, C:0.32, G:0.36, T:0.18
Consensus pattern (32 bp):
GCATGAGCCATGGTATGCCGCCTCCTGGGGCG
Found at i:14748 original size:33 final size:33
Alignment explanation
Indices: 14669--14750 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 33
14659 AGGGCGGTTA
* * *
14669 AGCCACGGCATGCCGCCCTCCTGGGGTGGCATG
1 AGCCAAGGCATGCCGTCCTCCTGGGGCGGCATG
* *
14702 AGCCATGGTATGCCGTCCTCCTGGGGCGGCAAAT-
1 AGCCAAGGCATGCCGTCCTCCTGGGGCGGC--ATG
14736 A-CCAAGGCATGCCGT
1 AGCCAAGGCATGCCGT
14751 TGATCAGACC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
33 38 0.93
34 1 0.02
35 2 0.05
ACGTcount: A:0.17, C:0.33, G:0.33, T:0.17
Consensus pattern (33 bp):
AGCCAAGGCATGCCGTCCTCCTGGGGCGGCATG
Found at i:14993 original size:9 final size:9
Alignment explanation
Indices: 14979--15004 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
14969 ATGATCGTGA
14979 TTGAAGAGC
1 TTGAAGAGC
14988 TTGAAGAGC
1 TTGAAGAGC
14997 TTGAAGAG
1 TTGAAGAG
15005 TCAATTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.08, G:0.35, T:0.23
Consensus pattern (9 bp):
TTGAAGAGC
Found at i:19309 original size:10 final size:10
Alignment explanation
Indices: 19294--19318 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
19284 GAGGACTCTA
19294 GAATTTTCTG
1 GAATTTTCTG
19304 GAATTTTCTG
1 GAATTTTCTG
19314 GAATT
1 GAATT
19319 GTGCAGGAAC
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:21226 original size:22 final size:23
Alignment explanation
Indices: 21174--21227 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
21164 AAATTAATTT
*
21174 TTAATTAATTAGTATTTAACTAC
1 TTAATTTATTAGTATTTAACTAC
* * *
21197 TTAGTTTATTAGT-TTTAATTAG
1 TTAATTTATTAGTATTTAACTAC
21219 TTAATTTAT
1 TTAATTTAT
21228 GATTAACTAC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 15 0.58
23 11 0.42
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.56
Consensus pattern (23 bp):
TTAATTTATTAGTATTTAACTAC
Found at i:21474 original size:21 final size:21
Alignment explanation
Indices: 21448--21488 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
21438 AGGGGGGGGG
**
21448 GGGGGGCGGTATTTAGCAAAA
1 GGGGGGCGGTAAATAGCAAAA
21469 GGGGGGCGGTAAATAGCAAA
1 GGGGGGCGGTAAATAGCAAA
21489 CCCCAGGCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.10, G:0.44, T:0.15
Consensus pattern (21 bp):
GGGGGGCGGTAAATAGCAAAA
Found at i:21945 original size:13 final size:13
Alignment explanation
Indices: 21924--21960 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
21914 GATAATTCTT
21924 TTTGACCCTCCAA
1 TTTGACCCTCCAA
*
21937 TTTGTCCCTCCAA
1 TTTGACCCTCCAA
*
21950 CTTGACCCTCC
1 TTTGACCCTCC
21961 TAATAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.16, C:0.43, G:0.08, T:0.32
Consensus pattern (13 bp):
TTTGACCCTCCAA
Found at i:22022 original size:41 final size:39
Alignment explanation
Indices: 21954--22042 Score: 124
Period size: 41 Copynumber: 2.2 Consensus size: 39
21944 CTCCAACTTG
* *
21954 ACCCTCCTAATAATTAAGGAAATAAATTAAATCCAGTTTT
1 ACCC-CCTAATAATTAAGGAAAGAAATTAAATCCAGGTTT
*
21994 AGCTCCCCTAATAATTAAGGTAAGAAATTAAATCCAGGTTT
1 A-C-CCCCTAATAATTAAGGAAAGAAATTAAATCCAGGTTT
22035 ACCCCCTA
1 ACCCCCTA
22043 GTTATAACTA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
39 6 0.14
40 2 0.05
41 34 0.77
42 2 0.05
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.29
Consensus pattern (39 bp):
ACCCCCTAATAATTAAGGAAAGAAATTAAATCCAGGTTT
Found at i:45157 original size:46 final size:46
Alignment explanation
Indices: 45090--45181 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
45080 TGATCAAAAG
*
45090 TACCTAAGAAAAATAAGTATAAAAGGTTTAGCTACTCATGGATTGC
1 TACCTAAGAAAAAGAAGTATAAAAGGTTTAGCTACTCATGGATTGC
45136 TACCTAAGAAAAAGAAGTATAAAAGGTTTAGCTACTCATGGATTGC
1 TACCTAAGAAAAAGAAGTATAAAAGGTTTAGCTACTCATGGATTGC
45182 AAGCAATCCA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.27
Consensus pattern (46 bp):
TACCTAAGAAAAAGAAGTATAAAAGGTTTAGCTACTCATGGATTGC
Done.