Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006907.1 Corchorus capsularis cultivar CVL-1 contig06928, 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: 17327
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Found at i:3981 original size:16 final size:16
Alignment explanation
Indices: 3960--3994 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
3950 CTAAAAATTC
*
3960 GGGTCATTTTTGGGTT
1 GGGTCAGTTTTGGGTT
3976 GGGTCAGTTTTGGGTT
1 GGGTCAGTTTTGGGTT
3992 GGG
1 GGG
3995 CGGGTTGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.06, C:0.06, G:0.46, T:0.43
Consensus pattern (16 bp):
GGGTCAGTTTTGGGTT
Found at i:4259 original size:18 final size:18
Alignment explanation
Indices: 4236--4272 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
4226 TAGGTGGATT
4236 TGTTAGCCACACTTTTTC
1 TGTTAGCCACACTTTTTC
4254 TGTTAGCCACACTTTTTC
1 TGTTAGCCACACTTTTTC
4272 T
1 T
4273 ATTTCCTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.27, G:0.11, T:0.46
Consensus pattern (18 bp):
TGTTAGCCACACTTTTTC
Found at i:9754 original size:20 final size:20
Alignment explanation
Indices: 9731--9796 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
9721 TCTGATTTGA
**
9731 CTTTTCTTCCTTTTTTATTT
1 CTTTTCTTAGTTTTTTATTT
**
9751 CTTTAATTAGTTTTTTATTT
1 CTTTTCTTAGTTTTTTATTT
*
9771 CTTTTCTTTTGTTTTTTATTT
1 CTTTTC-TTAGTTTTTTATTT
9792 CTTTT
1 CTTTT
9797 TTCTTTTCAC
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 20 0.53
21 18 0.47
ACGTcount: A:0.09, C:0.12, G:0.03, T:0.76
Consensus pattern (20 bp):
CTTTTCTTAGTTTTTTATTT
Found at i:9784 original size:21 final size:21
Alignment explanation
Indices: 9741--9796 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
9731 CTTTTCTTCC
9741 TTTTTTATTTC-TTTAATTAG
1 TTTTTTATTTCTTTTAATTAG
** *
9761 TTTTTTATTTCTTTTCTTTTG
1 TTTTTTATTTCTTTTAATTAG
9782 TTTTTTATTTCTTTT
1 TTTTTTATTTCTTTT
9797 TTCTTTTCAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 11 0.34
21 21 0.66
ACGTcount: A:0.11, C:0.07, G:0.04, T:0.79
Consensus pattern (21 bp):
TTTTTTATTTCTTTTAATTAG
Found at i:10474 original size:38 final size:38
Alignment explanation
Indices: 10432--10558 Score: 141
Period size: 38 Copynumber: 3.3 Consensus size: 38
10422 ACGAGAATGA
* * *
10432 AACTCTGAATAGATGCTTAAGCTGGTTTTCTTAAGCGG
1 AACTCTAAATAGATGCCTAAGCTGGTTTTCTTAAACGG
* *
10470 AACTCTAAATAGA-GACCTAA-ATCAGTTTTCTTAAACGG
1 AACTCTAAATAGATG-CCTAAGCT-GGTTTTCTTAAACGG
* * * *
10508 AACTCTAAACAAATACCTAAGCAGGTTTTCTTAAACGG
1 AACTCTAAATAGATGCCTAAGCTGGTTTTCTTAAACGG
10546 AACTCTAAATAGA
1 AACTCTAAATAGA
10559 GACCTTAAAT
Statistics
Matches: 72, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
37 2 0.03
38 70 0.97
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (38 bp):
AACTCTAAATAGATGCCTAAGCTGGTTTTCTTAAACGG
Found at i:10512 original size:76 final size:77
Alignment explanation
Indices: 10378--10568 Score: 217
Period size: 76 Copynumber: 2.5 Consensus size: 77
10368 AAATCTAGAT
** * * * *
10378 AGGTTTTCTTAAACATAACTCTAAATAGAGACCTAAA-GAGATTTACGAGAATGAAACTCTGAAT
1 AGGTTTTCTTAAACGGAACTCTAAATAGAGACCTAAATCAGATTTACGAGAACGAAACTCTAAAC
* * *
10442 AGATGCTTAAGC
66 AAATACCTAAGC
* * * * *
10454 TGGTTTTCTTAAGCGGAACTCTAAATAGAGACCTAAATCAG-TTTTCTTA-AACGGAACTCTAAA
1 AGGTTTTCTTAAACGGAACTCTAAATAGAGACCTAAATCAGATTTAC-GAGAACGAAACTCTAAA
10517 CAAATACCTAAGC
65 CAAATACCTAAGC
10530 AGGTTTTCTTAAACGGAACTCTAAATAGAGACCTTAAAT
1 AGGTTTTCTTAAACGGAACTCTAAATAGAGACC-TAAAT
10569 TGTAACTCCA
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
76 88 0.92
77 8 0.08
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.29
Consensus pattern (77 bp):
AGGTTTTCTTAAACGGAACTCTAAATAGAGACCTAAATCAGATTTACGAGAACGAAACTCTAAAC
AAATACCTAAGC
Found at i:10632 original size:64 final size:64
Alignment explanation
Indices: 10508--10632 Score: 162
Period size: 64 Copynumber: 2.0 Consensus size: 64
10498 TCTTAAACGG
* * * *
10508 AACTCTAAACAAATACCTAAGCAGGTTTTCTTAAACGGAACTCTAAATAGAGACCTTAAATTGT
1 AACTCCAAACAAAGACCTAAGCAGGTTTACTTAAACGGAACTCTAAACAGAGACCTTAAATTGT
* * * *
10572 AACTCCAAACAGAGACCTAAGCAGGTTTACTTAAATGGAAATTTTAAACAGAGACC-TAAAT
1 AACTCCAAACAAAGACCTAAGCAGGTTTACTTAAACGG-AACTCTAAACAGAGACCTTAAAT
10633 AGGTTTACTT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
64 38 0.73
65 14 0.27
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (64 bp):
AACTCCAAACAAAGACCTAAGCAGGTTTACTTAAACGGAACTCTAAACAGAGACCTTAAATTGT
Found at i:10665 original size:77 final size:77
Alignment explanation
Indices: 10562--10779 Score: 328
Period size: 77 Copynumber: 2.8 Consensus size: 77
10552 AAATAGAGAC
* * * * * * *
10562 CTTAAATTGTAACTCCAAACAGAGACCTAAGCAGGTTTACTTAAATGGAAATTTTAAACAGAGAC
1 CTTAAA-TGAAACTCTAAATAGAGACCTGAGCAGGTTTACTTAAATGAAAACTCTAAACAGAGAC
*
10627 CTAAATAGGTTTA
65 CTAAACAGGTTTA
10640 CTTAAATGAAACTCTAAATAGAGACCTGAGCAGGTTTACTTAAATGAAAACTCTAAACAGAGACC
1 CTTAAATGAAACTCTAAATAGAGACCTGAGCAGGTTTACTTAAATGAAAACTCTAAACAGAGACC
*
10705 TAAGCAGGTTTA
66 TAAACAGGTTTA
* *
10717 CTTACATGAAACTCTAAATAGAGACCTGAGCAGGTTTATTTAAATGAAAACTCTAAACAGAGA
1 CTTAAATGAAACTCTAAATAGAGACCTGAGCAGGTTTACTTAAATGAAAACTCTAAACAGAGA
10780 AAAACAATCA
Statistics
Matches: 129, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
77 123 0.95
78 6 0.05
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (77 bp):
CTTAAATGAAACTCTAAATAGAGACCTGAGCAGGTTTACTTAAATGAAAACTCTAAACAGAGACC
TAAACAGGTTTA
Found at i:10675 original size:38 final size:38
Alignment explanation
Indices: 10562--10779 Score: 292
Period size: 39 Copynumber: 5.6 Consensus size: 38
10552 AAATAGAGAC
* *
10562 CTTAAATTGTAACTCCAAACAGAGACCTAAGCAGGTTTA
1 CTTAAA-TGAAACTCTAAACAGAGACCTAAGCAGGTTTA
* * **
10601 CTTAAATGGAAATTTTAAACAGAGACCTAAATAGGTTTA
1 CTTAAAT-GAAACTCTAAACAGAGACCTAAGCAGGTTTA
* *
10640 CTTAAATGAAACTCTAAATAGAGACCTGAGCAGGTTTA
1 CTTAAATGAAACTCTAAACAGAGACCTAAGCAGGTTTA
10678 CTTAAATGAAAACTCTAAACAGAGACCTAAGCAGGTTTA
1 CTTAAATG-AAACTCTAAACAGAGACCTAAGCAGGTTTA
* * *
10717 CTTACATGAAACTCTAAATAGAGACCTGAGCAGGTTTA
1 CTTAAATGAAACTCTAAACAGAGACCTAAGCAGGTTTA
*
10755 TTTAAATGAAAACTCTAAACAGAGA
1 CTTAAATG-AAACTCTAAACAGAGA
10780 AAAACAATCA
Statistics
Matches: 156, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
38 68 0.44
39 88 0.56
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (38 bp):
CTTAAATGAAACTCTAAACAGAGACCTAAGCAGGTTTA
Found at i:15209 original size:2 final size:2
Alignment explanation
Indices: 15202--15232 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
15192 AGATAACAAG
*
15202 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15233 GAAAATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Done.