Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013978.1 Corchorus capsularis cultivar CVL-1 contig13999, 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: 8258
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Found at i:4852 original size:21 final size:21
Alignment explanation
Indices: 4826--4865 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4816 ACGAGATTAC
4826 ACTGTATAGACCAAATTATAT
1 ACTGTATAGACCAAATTATAT
* *
4847 ACTGTATAGATCAGATTAT
1 ACTGTATAGACCAAATTAT
4866 TAGAGTAGCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (21 bp):
ACTGTATAGACCAAATTATAT
Found at i:5210 original size:480 final size:480
Alignment explanation
Indices: 4309--5268 Score: 1911
Period size: 480 Copynumber: 2.0 Consensus size: 480
4299 AGAACGGTGT
*
4309 GATTGACTATGTTTAGATACTGCATAGACGAGATTACATTGTATAGACCAAATTATATACTGTAT
1 GATTGACTATGTTTAGATACTGCATAGACGAGATTACACTGTATAGACCAAATTATATACTGTAT
4374 AGATCAGATTATTAGAGTAGCGATAGAAACGGAGATTGCACTTAAAGCTCCTTTTGATCGGTTCA
66 AGATCAGATTATTAGAGTAGCGATAGAAACGGAGATTGCACTTAAAGCTCCTTTTGATCGGTTCA
4439 AGCCTAAATCAATTTAATTTTGGGTTTTTAATTAAAATAGAAAATATAAGATATTGTGATGATGT
131 AGCCTAAATCAATTTAATTTTGGGTTTTTAATTAAAATAGAAAATATAAGATATTGTGATGATGT
4504 GGCACAAAAACACTATAAATTGAGAAATAATTTTAAAAGTACAAACACTTTGGGAATTAAGTTTT
196 GGCACAAAAACACTATAAATTGAGAAATAATTTTAAAAGTACAAACACTTTGGGAATTAAGTTTT
4569 CAAACTATAATAGATTAGTAGAAACTCCTTTTAAAAATACAAAAATAAATAAATTTCTTCTACAT
261 CAAACTATAATAGATTAGTAGAAACTCCTTTTAAAAATACAAAAATAAATAAATTTCTTCTACAT
4634 ATTTCAATATATTCATCAATACAAAAGAAAAATAAAAAAAGAGTAAATATGATGTTAGAAATGGC
326 ATTTCAATATATTCATCAATACAAAAGAAAAATAAAAAAAGAGTAAATATGATGTTAGAAATGGC
4699 TAATAATGATATCATGAAGGATATTATAATTATATACACAAAATTAAATAATTATGTAAAGCTAT
391 TAATAATGATATCATGAAGGATATTATAATTATATACACAAAATTAAATAATTATGTAAAGCTAT
4764 AAAATGCTTAATTAGTAAACCGAAA
456 AAAATGCTTAATTAGTAAACCGAAA
4789 GATTGACTATGTTTAGATACTGCATAGACGAGATTACACTGTATAGACCAAATTATATACTGTAT
1 GATTGACTATGTTTAGATACTGCATAGACGAGATTACACTGTATAGACCAAATTATATACTGTAT
4854 AGATCAGATTATTAGAGTAGCGATAGAAACGGAGATTGCACTTAAAGCTCCTTTTGATCGGTTCA
66 AGATCAGATTATTAGAGTAGCGATAGAAACGGAGATTGCACTTAAAGCTCCTTTTGATCGGTTCA
4919 AGCCTAAATCAATTTAATTTTGGGTTTTTAATTAAAATAGAAAATATAAGATATTGTGATGATGT
131 AGCCTAAATCAATTTAATTTTGGGTTTTTAATTAAAATAGAAAATATAAGATATTGTGATGATGT
4984 GGCACAAAAACACTATAAATTGAGAAATAATTTTAAAAGTACAAACACTTTGGGAATTAAGTTTT
196 GGCACAAAAACACTATAAATTGAGAAATAATTTTAAAAGTACAAACACTTTGGGAATTAAGTTTT
5049 CAAACTATAATAGATTAGTAGAAACTCCTTTTAAAAATACAAAAATAAATAAATTTCTTCTACAT
261 CAAACTATAATAGATTAGTAGAAACTCCTTTTAAAAATACAAAAATAAATAAATTTCTTCTACAT
5114 ATTTCAATATATTCATCAATACAAAAGAAAAATAAAAAAAGAGTAAATATGATGTTAGAAATGGC
326 ATTTCAATATATTCATCAATACAAAAGAAAAATAAAAAAAGAGTAAATATGATGTTAGAAATGGC
5179 TAATAATGATATCATGAAGGATATTATAATTATATACACAAAATTAAATAATTATGTAAAGCTAT
391 TAATAATGATATCATGAAGGATATTATAATTATATACACAAAATTAAATAATTATGTAAAGCTAT
5244 AAAATGCTTAATTAGTAAACCGAAA
456 AAAATGCTTAATTAGTAAACCGAAA
5269 ATGACCCTTA
Statistics
Matches: 479, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
480 479 1.00
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.32
Consensus pattern (480 bp):
GATTGACTATGTTTAGATACTGCATAGACGAGATTACACTGTATAGACCAAATTATATACTGTAT
AGATCAGATTATTAGAGTAGCGATAGAAACGGAGATTGCACTTAAAGCTCCTTTTGATCGGTTCA
AGCCTAAATCAATTTAATTTTGGGTTTTTAATTAAAATAGAAAATATAAGATATTGTGATGATGT
GGCACAAAAACACTATAAATTGAGAAATAATTTTAAAAGTACAAACACTTTGGGAATTAAGTTTT
CAAACTATAATAGATTAGTAGAAACTCCTTTTAAAAATACAAAAATAAATAAATTTCTTCTACAT
ATTTCAATATATTCATCAATACAAAAGAAAAATAAAAAAAGAGTAAATATGATGTTAGAAATGGC
TAATAATGATATCATGAAGGATATTATAATTATATACACAAAATTAAATAATTATGTAAAGCTAT
AAAATGCTTAATTAGTAAACCGAAA
Found at i:8106 original size:48 final size:48
Alignment explanation
Indices: 8027--8253 Score: 208
Period size: 49 Copynumber: 4.7 Consensus size: 48
8017 AAGTGAACTT
* * * *
8027 GCCTTTCGTCCGGAAAGGGCATCTTAAGAAAAAGCGAA-TAAAACTAA-C
1 GCCTTCCGTCCGGGAAGGGCATTTTAGGAAAAAGC-AAGTAAAA-TAAGC
* * * *
8075 GCCTTCCGTCCGGGAAGGGCGTTTTAGGAAAAAGCAAGTAAGAGTTAGT
1 GCCTTCCGTCCGGGAAGGGCATTTTAGGAAAAAGCAAGTAA-AATAAGC
* * * **
8124 GCTTTCCGTCCGGGAAGGGCACTTTGGGAAAAAGTGAGTAAAATAAGC
1 GCCTTCCGTCCGGGAAGGGCATTTTAGGAAAAAGCAAGTAAAATAAGC
* * * * *
8172 GTCTTCCGCCCGGGAAGAGCATTTTTGGAAAAATAGCAAGT-AAATAAGT
1 GCCTTCCGTCCGGGAAGGGCATTTTAGG-AAAA-AGCAAGTAAAATAAGC
* *
8221 GCCTCCCGTCCGGGAAGGGCATTTTGGGAAAAA
1 GCCTTCCGTCCGGGAAGGGCATTTTAGGAAAAA
8254 CAGGT
Statistics
Matches: 143, Mismatches: 31, Indels: 11
0.77 0.17 0.06
Matches are distributed among these distances:
47 3 0.02
48 65 0.45
49 70 0.49
50 5 0.03
ACGTcount: A:0.32, C:0.19, G:0.28, T:0.21
Consensus pattern (48 bp):
GCCTTCCGTCCGGGAAGGGCATTTTAGGAAAAAGCAAGTAAAATAAGC
Found at i:8202 original size:97 final size:96
Alignment explanation
Indices: 8029--8253 Score: 251
Period size: 97 Copynumber: 2.3 Consensus size: 96
8019 GTGAACTTGC
* ** * *
8029 CTTT-CGTCCGGAAAGGGCATCTTAAGAAAAAGCGAATAAAACTAACGCCTTCCGTCCGGGAAGG
1 CTTTCCGTCCGGGAAGGGCAT-TTGGGAAAAAGCGAATAAAACTAACGCCTTCCGCCCGGGAAGA
* *
8093 GCGTTTTAGG-AAAA-AGCAAGTAAGAGTTAGTG
65 GCATTTTAGGAAAAATAGCAAGTAA-A-TAAGTG
* * *
8125 CTTTCCGTCCGGGAAGGGCACTTTGGGAAAAAGTGAGTAAAA-TAAGCGTCTTCCGCCCGGGAAG
1 CTTTCCGTCCGGGAAGGGCA-TTTGGGAAAAAGCGAATAAAACTAA-CGCCTTCCGCCCGGGAAG
*
8189 AGCATTTTTGGAAAAATAGCAAGTAAATAAGTG
64 AGCATTTTAGGAAAAATAGCAAGTAAATAAGTG
* *
8222 CCTCCCGTCCGGGAAGGGCATTTTGGGAAAAA
1 CTTTCCGTCCGGGAAGGGCA-TTTGGGAAAAA
8254 CAGGT
Statistics
Matches: 110, Mismatches: 14, Indels: 9
0.83 0.11 0.07
Matches are distributed among these distances:
96 7 0.06
97 88 0.80
98 6 0.05
99 9 0.08
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.21
Consensus pattern (96 bp):
CTTTCCGTCCGGGAAGGGCATTTGGGAAAAAGCGAATAAAACTAACGCCTTCCGCCCGGGAAGAG
CATTTTAGGAAAAATAGCAAGTAAATAAGTG
Done.