Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007667.1 Corchorus capsularis cultivar CVL-1 contig07688, 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: 24869
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:119 original size:26 final size:26
Alignment explanation
Indices: 77--135 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
67 TGCCTCTCTC
* * **
77 TTTTTTTCTTTCTTTCTTTTTTTGTT
1 TTTTTTTCTTTCGTTCTTCTTTAATT
103 TTTTTTTCTCTT-GTTCTTCTTTAATT
1 TTTTTTTCT-TTCGTTCTTCTTTAATT
129 TTTTTTT
1 TTTTTTT
136 AAAGATTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 26 0.93
27 2 0.07
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.81
Consensus pattern (26 bp):
TTTTTTTCTTTCGTTCTTCTTTAATT
Found at i:2601 original size:18 final size:18
Alignment explanation
Indices: 2578--2612 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2568 TAATATCACC
2578 AGCAAGAAGAAGAAAAGT
1 AGCAAGAAGAAGAAAAGT
2596 AGCAAGAAGAAGAAAAG
1 AGCAAGAAGAAGAAAAG
2613 AGAAGAGTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.63, C:0.06, G:0.29, T:0.03
Consensus pattern (18 bp):
AGCAAGAAGAAGAAAAGT
Found at i:9549 original size:1 final size:1
Alignment explanation
Indices: 9543--9599 Score: 78
Period size: 1 Copynumber: 57.0 Consensus size: 1
9533 AATGATTGTC
* * * *
9543 AAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAACAAAAAAAAACAAAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
9600 GGAGAACAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:9562 original size:16 final size:16
Alignment explanation
Indices: 9543--9599 Score: 89
Period size: 16 Copynumber: 3.6 Consensus size: 16
9533 AATGATTGTC
9543 AAAAAAAAAAAAA-AA
1 AAAAAAAAAAAAACAA
9558 AAAAAAAAAAAAACAA
1 AAAAAAAAAAAAACAA
*
9574 AAACAAAAAAAAACAA
1 AAAAAAAAAAAAACAA
*
9590 AAAAACAAAA
1 AAAAAAAAAA
9600 GGAGAACAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
15 13 0.34
16 25 0.66
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAACAA
Found at i:9608 original size:29 final size:29
Alignment explanation
Indices: 9542--9599 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 29
9532 AAATGATTGT
*
9542 CAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 CAAAAAAAAAAAAAAAAAAAAAACAAAAA
*
9571 CAAAAACAAAAAAAAACAAAAAAACAAAA
1 CAAAAA-AAAAAAAAAAAAAAAAACAAAA
9600 GGAGAACAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (29 bp):
CAAAAAAAAAAAAAAAAAAAAAACAAAAA
Found at i:9608 original size:35 final size:29
Alignment explanation
Indices: 9542--9599 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
9532 AAATGATTGT
9542 CAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 CAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
9571 CAAAAACAAAAAAAAACAAAAAAACAAAA
1 CAAAAAAAAAAAAAAAAAAAAAAAAAAAA
9600 GGAGAACAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (29 bp):
CAAAAAAAAAAAAAAAAAAAAAAAAAAAA
Found at i:12117 original size:18 final size:18
Alignment explanation
Indices: 12081--12118 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
12071 TATTTTATTT
*
12081 TTTATTTCTTCATTTTTC
1 TTTATTTCTTCATTCTTC
12099 TTTATTTTCTTC-TTCTTC
1 TTTA-TTTCTTCATTCTTC
12117 TT
1 TT
12119 CTTCTTCTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTTCTTCATTCTTC
Found at i:13066 original size:3 final size:3
Alignment explanation
Indices: 13058--13082 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
13048 ATTTTGAGAG
13058 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
13083 TTGTTTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:14690 original size:26 final size:26
Alignment explanation
Indices: 14652--14708 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
14642 GAGGTGGTAA
**
14652 TCGGGCGGGTCAGGTTGATTTCGGGT
1 TCGGGCGGGTCAGGTCAATTTCGGGT
14678 TCGGG-GGGTTCAGGTCAATTTCGGGT
1 TCGGGCGGG-TCAGGTCAATTTCGGGT
14704 TCGGG
1 TCGGG
14709 TTTGAGTTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 3 0.11
26 25 0.89
ACGTcount: A:0.09, C:0.16, G:0.46, T:0.30
Consensus pattern (26 bp):
TCGGGCGGGTCAGGTCAATTTCGGGT
Found at i:14761 original size:32 final size:32
Alignment explanation
Indices: 14717--14786 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
14707 GGTTTGAGTT
14717 AGGTT-GGATTAAATTTGGGTAAGATCGATTC
1 AGGTTCGGATTAAATTTGGGTAAGATCGATTC
* * * *
14748 AGGTTCGGGTTAAATTTGGGTCAGGTTGATTC
1 AGGTTCGGATTAAATTTGGGTAAGATCGATTC
*
14780 GGGTTCG
1 AGGTTCG
14787 AGTCAATTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
31 5 0.15
32 28 0.85
ACGTcount: A:0.21, C:0.09, G:0.34, T:0.36
Consensus pattern (32 bp):
AGGTTCGGATTAAATTTGGGTAAGATCGATTC
Found at i:14798 original size:32 final size:32
Alignment explanation
Indices: 14743--14817 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
14733 GGGTAAGATC
* * * * *
14743 GATTCAGGTTCGGGTTAAATTTGGGTCAGGTT
1 GATTCGGGTTCGAGTCAAATTTGGGCCAAGTT
*
14775 GATTCGGGTTCGAGTCAATTTTGGGCCAAGTT
1 GATTCGGGTTCGAGTCAAATTTGGGCCAAGTT
*
14807 GATTTGGGTTC
1 GATTCGGGTTC
14818 AAGTTCGCTC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.17, C:0.12, G:0.33, T:0.37
Consensus pattern (32 bp):
GATTCGGGTTCGAGTCAAATTTGGGCCAAGTT
Found at i:15067 original size:32 final size:32
Alignment explanation
Indices: 15022--15099 Score: 129
Period size: 32 Copynumber: 2.4 Consensus size: 32
15012 TTTTTTCAGG
*
15022 TTCAGGTTCGGGTTTTATCGGATTTTAGATTT
1 TTCAGGTTCGGGTTTTATCGGATTTGAGATTT
* *
15054 TTCGGGTTCGGGTTTTATCGGGTTTGAGATTT
1 TTCAGGTTCGGGTTTTATCGGATTTGAGATTT
15086 TTCAGGTTCGGGTT
1 TTCAGGTTCGGGTT
15100 CGGGTTCGGA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.12, C:0.10, G:0.31, T:0.47
Consensus pattern (32 bp):
TTCAGGTTCGGGTTTTATCGGATTTGAGATTT
Found at i:15074 original size:16 final size:15
Alignment explanation
Indices: 15051--15099 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
15041 GGATTTTAGA
15051 TTTTTCGGGTTCGGG
1 TTTTTCGGGTTCGGG
* *
15066 TTTTATCGGGTTTGAGA
1 TTTT-TCGGGTTCG-GG
*
15083 TTTTTCAGGTTCGGG
1 TTTTTCGGGTTCGGG
15098 TT
1 TT
15100 CGGGTTCGGA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
15 7 0.26
16 15 0.56
17 5 0.19
ACGTcount: A:0.08, C:0.10, G:0.33, T:0.49
Consensus pattern (15 bp):
TTTTTCGGGTTCGGG
Found at i:19056 original size:18 final size:18
Alignment explanation
Indices: 19033--19068 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
19023 TCGAATACGT
*
19033 TTTGCCTCAATTAGACGG
1 TTTGCCCCAATTAGACGG
*
19051 TTTGCCCCTATTAGACGG
1 TTTGCCCCAATTAGACGG
19069 GATTTCTGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.33
Consensus pattern (18 bp):
TTTGCCCCAATTAGACGG
Found at i:20216 original size:26 final size:27
Alignment explanation
Indices: 20186--20240 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
20176 AGCACTTGTG
20186 GTGAGCTT-GGAGAAGCTCGGTTGTTT
1 GTGAGCTTAGGAGAAGCTCGGTTGTTT
** *
20212 GTGAGCTTAGTTGAAGCTCGGTTTTTT
1 GTGAGCTTAGGAGAAGCTCGGTTGTTT
20239 GT
1 GT
20241 AAATGCTTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 8 0.32
27 17 0.68
ACGTcount: A:0.15, C:0.11, G:0.35, T:0.40
Consensus pattern (27 bp):
GTGAGCTTAGGAGAAGCTCGGTTGTTT
Found at i:20401 original size:15 final size:15
Alignment explanation
Indices: 20381--20419 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
20371 AAACCGATAA
20381 AGTCGGGTTCGGTGC
1 AGTCGGGTTCGGTGC
*
20396 AGTCGGGCTCGGTGC
1 AGTCGGGTTCGGTGC
*
20411 AATCGGGTT
1 AGTCGGGTT
20420 TGAAACTCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.10, C:0.21, G:0.44, T:0.26
Consensus pattern (15 bp):
AGTCGGGTTCGGTGC
Found at i:20709 original size:30 final size:30
Alignment explanation
Indices: 20673--20747 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
20663 AGAGGATGCT
* **
20673 ATCGCACAAGACCGGCCATTGCATGGAG-GG
1 ATCGCACAAGACCGGCCATGGCATGG-GCCA
*
20703 ATCGCACATGACCGGCCATGGCATGGGCCA
1 ATCGCACAAGACCGGCCATGGCATGGGCCA
20733 ATCGCACAAGACCGG
1 ATCGCACAAGACCGG
20748 GCACAACCAG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 1 0.03
30 38 0.97
ACGTcount: A:0.27, C:0.31, G:0.31, T:0.12
Consensus pattern (30 bp):
ATCGCACAAGACCGGCCATGGCATGGGCCA
Found at i:22264 original size:36 final size:37
Alignment explanation
Indices: 22196--22266 Score: 119
Period size: 37 Copynumber: 1.9 Consensus size: 37
22186 AAAAGGCCGC
22196 CGGTGTCGGAGATCGAAGAAGGGAGGAGACTGAGTGT
1 CGGTGTCGGAGATCGAAGAAGGGAGGAGACTGAGTGT
22233 CGGTGTCGGAGATC-AGAGAA-GGAGGAGACTGAGT
1 CGGTGTCGGAGATCGA-AGAAGGGAGGAGACTGAGT
22267 ATGGGTTCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
36 15 0.45
37 18 0.55
ACGTcount: A:0.28, C:0.11, G:0.45, T:0.15
Consensus pattern (37 bp):
CGGTGTCGGAGATCGAAGAAGGGAGGAGACTGAGTGT
Found at i:23261 original size:223 final size:223
Alignment explanation
Indices: 22873--23318 Score: 840
Period size: 223 Copynumber: 2.0 Consensus size: 223
22863 CTATTGCACA
22873 TTCAACTTGTTCATTTACTCTCTTTGTCATATCCATTTTCTACATTTTCCACTGCACAGTTTTTC
1 TTCAACTTGTTCATTTACTCTCTTTGTCATATCCATTTTCTACATTTTCCACTGCACAGTTTTTC
22938 ATTGCTCCCATAAATTGTTTCATATACTCTAGTCGTACTAACGATATGTCTTGCAGAAAAATTAG
66 ATTGCTCCCATAAATTGTTTCATATACTCTAGTCGTACTAACGATATGTCTTGCAGAAAAATTAG
*
23003 TTAAGTCAAAAGTAAGTGTTAGGTGAGACTTTGGGACCAACACCACCTTTGCCACCACCTTTGGG
131 TTAAGCCAAAAGTAAGTGTTAGGTGAGACTTTGGGACCAACACCACCTTTGCCACCACCTTTGGG
*
23068 ACCAACAGTAGCTACCTGACGTGCTTTG
196 ACCAACAGTAGCTACCTGACGCGCTTTG
23096 TTCAACTTGTTCATTTACTCT-TCTTGTCATATCCATTTTCTACATTTTCCACTGCACAGTTTTT
1 TTCAACTTGTTCATTTACTCTCT-TTGTCATATCCATTTTCTACATTTTCCACTGCACAGTTTTT
* *
23160 CATTGCTCCCATAAATTGTTTCATATACTCTGGTCGTACTAACGATATGTCTTGTAGAAAAATTA
65 CATTGCTCCCATAAATTGTTTCATATACTCTAGTCGTACTAACGATATGTCTTGCAGAAAAATTA
23225 GTTAAGCCAAAAGTAAGTGTTAGGTGAGACTTTGGGACCAACACCACCTTTGCCACCACCTTTGG
130 GTTAAGCCAAAAGTAAGTGTTAGGTGAGACTTTGGGACCAACACCACCTTTGCCACCACCTTTGG
23290 GACCAACAGTAGCTACCTGACGCGCTTTG
195 GACCAACAGTAGCTACCTGACGCGCTTTG
23319 AAATCCCAGA
Statistics
Matches: 218, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
222 1 0.00
223 217 1.00
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (223 bp):
TTCAACTTGTTCATTTACTCTCTTTGTCATATCCATTTTCTACATTTTCCACTGCACAGTTTTTC
ATTGCTCCCATAAATTGTTTCATATACTCTAGTCGTACTAACGATATGTCTTGCAGAAAAATTAG
TTAAGCCAAAAGTAAGTGTTAGGTGAGACTTTGGGACCAACACCACCTTTGCCACCACCTTTGGG
ACCAACAGTAGCTACCTGACGCGCTTTG
Done.