Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007401.1 Corchorus capsularis cultivar CVL-1 contig07422, 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: 35899
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:42 original size:32 final size:32
Alignment explanation
Indices: 1--133 Score: 212
Period size: 32 Copynumber: 4.2 Consensus size: 32
1 GGCCTGCCGTGGCGAAGCCTCCCCACCGGGGC
1 GGCCTGCCGTGGCGAAGCCTCCCCACCGGGGC
33 GGCCTGCCGTGGCGAAGCCTCCCCACCGGGGC
1 GGCCTGCCGTGGCGAAGCCTCCCCACCGGGGC
*
65 GGCCTGCCGTGGCGAAGCCTCCCCACCGGGAC
1 GGCCTGCCGTGGCGAAGCCTCCCCACCGGGGC
* * * **
97 GGCCTGCCCTGGCTAAGCCGCCCCAGTGGGGC
1 GGCCTGCCGTGGCGAAGCCTCCCCACCGGGGC
129 GGCCT
1 GGCCT
134 TTTCATGGGG
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 94 1.00
ACGTcount: A:0.10, C:0.43, G:0.37, T:0.11
Consensus pattern (32 bp):
GGCCTGCCGTGGCGAAGCCTCCCCACCGGGGC
Found at i:13896 original size:247 final size:247
Alignment explanation
Indices: 13460--13954 Score: 990
Period size: 247 Copynumber: 2.0 Consensus size: 247
13450 AACTTATCTA
13460 TATGTGTGTGTGAGTGTGTGTTCTTAAAAACAATAGTGATGTTGGAAGAAAAGCCATAAAAAGTT
1 TATGTGTGTGTGAGTGTGTGTTCTTAAAAACAATAGTGATGTTGGAAGAAAAGCCATAAAAAGTT
13525 AGTATGATCAGCAAATTATGAGATATGAGGATTCTTATTTCCATAATATATTCATTCTTTTATAT
66 AGTATGATCAGCAAATTATGAGATATGAGGATTCTTATTTCCATAATATATTCATTCTTTTATAT
13590 GTATGGAAATAAACTACAGCATGAAAAGTCACATTCTCAGCCAAAACAGCAACCGAATATTAGAT
131 GTATGGAAATAAACTACAGCATGAAAAGTCACATTCTCAGCCAAAACAGCAACCGAATATTAGAT
13655 ATCTCAAAATACCCAAAGCAACACACCATAAATATCGAATATGTAAACTTGG
196 ATCTCAAAATACCCAAAGCAACACACCATAAATATCGAATATGTAAACTTGG
13707 TATGTGTGTGTGAGTGTGTGTTCTTAAAAACAATAGTGATGTTGGAAGAAAAGCCATAAAAAGTT
1 TATGTGTGTGTGAGTGTGTGTTCTTAAAAACAATAGTGATGTTGGAAGAAAAGCCATAAAAAGTT
13772 AGTATGATCAGCAAATTATGAGATATGAGGATTCTTATTTCCATAATATATTCATTCTTTTATAT
66 AGTATGATCAGCAAATTATGAGATATGAGGATTCTTATTTCCATAATATATTCATTCTTTTATAT
13837 GTATGGAAATAAACTACAGCATGAAAAGTCACATTCTCAGCCAAAACAGCAACCGAATATTAGAT
131 GTATGGAAATAAACTACAGCATGAAAAGTCACATTCTCAGCCAAAACAGCAACCGAATATTAGAT
13902 ATCTCAAAATACCCAAAGCAACACACCATAAATATCGAATATGTAAACTTGG
196 ATCTCAAAATACCCAAAGCAACACACCATAAATATCGAATATGTAAACTTGG
13954 T
1 T
13955 CAATGAGAGT
Statistics
Matches: 248, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
247 248 1.00
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.30
Consensus pattern (247 bp):
TATGTGTGTGTGAGTGTGTGTTCTTAAAAACAATAGTGATGTTGGAAGAAAAGCCATAAAAAGTT
AGTATGATCAGCAAATTATGAGATATGAGGATTCTTATTTCCATAATATATTCATTCTTTTATAT
GTATGGAAATAAACTACAGCATGAAAAGTCACATTCTCAGCCAAAACAGCAACCGAATATTAGAT
ATCTCAAAATACCCAAAGCAACACACCATAAATATCGAATATGTAAACTTGG
Found at i:26599 original size:30 final size:30
Alignment explanation
Indices: 26565--26639 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
26555 GGTCATGTGC
* * * *
26565 CCGGTCTTGTGCGGTTACTTCATGCAATGG
1 CCGGTCTTGTGCGATGACTCCATCCAATGG
*
26595 CCGGTCTTGTGCGATGGCTCCATCCAATGG
1 CCGGTCTTGTGCGATGACTCCATCCAATGG
* *
26625 CCGGTCATATGCGAT
1 CCGGTCTTGTGCGAT
26640 CCCATCATCT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.15, C:0.27, G:0.29, T:0.29
Consensus pattern (30 bp):
CCGGTCTTGTGCGATGACTCCATCCAATGG
Found at i:34646 original size:24 final size:23
Alignment explanation
Indices: 34613--34672 Score: 97
Period size: 24 Copynumber: 2.7 Consensus size: 23
34603 GAAAAATGGA
34613 AAAAACTTTTTTTTTATCGACGC
1 AAAAACTTTTTTTTTATCGACGC
34636 AAAAACATTTTTTTTTATCGACGC
1 AAAAAC-TTTTTTTTTATCGACGC
34660 --AAACTTTTTTTTT
1 AAAAACTTTTTTTTT
34673 TTTAGAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
21 9 0.25
22 4 0.11
23 6 0.17
24 17 0.47
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.48
Consensus pattern (23 bp):
AAAAACTTTTTTTTTATCGACGC
Found at i:35003 original size:27 final size:26
Alignment explanation
Indices: 34943--35004 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 26
34933 AAATCAATTA
34943 TAAAG-AAAACAATTAAACTAAAAATC
1 TAAAGCAAAACAATTAAACT-AAAATC
*
34969 -AAAACAAAACAAATTAAATCT-AAATC
1 TAAAGCAAAAC-AATTAAA-CTAAAATC
34995 TAAAGCAAAA
1 TAAAGCAAAA
35005 TATTAAAGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
25 3 0.10
26 10 0.33
27 15 0.50
28 2 0.07
ACGTcount: A:0.66, C:0.13, G:0.03, T:0.18
Consensus pattern (26 bp):
TAAAGCAAAACAATTAAACTAAAATC
Done.