Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015799.1 Corchorus capsularis cultivar CVL-1 contig15820, 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: 10321
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Found at i:2924 original size:33 final size:32
Alignment explanation
Indices: 2826--2999 Score: 168
Period size: 33 Copynumber: 5.3 Consensus size: 32
2816 AAAGGATCAT
* ** * **
2826 GTGGCCGGTTATGGCCGGGCATGGCCGAGTCAT
1 GTGGCCGG-TGTGGCCGGGCATCTCCAAGTCGC
** * *
2859 GTGGCCGGTTGTGGCCGGGCATGGCTATGTCGC
1 GTGGCCGG-TGTGGCCGGGCATCTCCAAGTCGC
2892 GTGGCCGGTGATGGCCGGGCATCTCCAAGTCGC
1 GTGGCCGGTG-TGGCCGGGCATCTCCAAGTCGC
* *
2925 GTGGCCGGTGTTGCTCGGGCATCTCCAACTCGC
1 GTGGCCGGTGTGGC-CGGGCATCTCCAAGTCGC
* *
2958 GTGGCCGGTGTTGCACGGTCATCTCCAAGTCGC
1 GTGGCCGGTGTGGC-CGGGCATCTCCAAGTCGC
*
2991 ATGGCCGGT
1 GTGGCCGGT
3000 CACAAGTGCT
Statistics
Matches: 123, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
32 5 0.04
33 118 0.96
ACGTcount: A:0.10, C:0.28, G:0.39, T:0.22
Consensus pattern (32 bp):
GTGGCCGGTGTGGCCGGGCATCTCCAAGTCGC
Found at i:5137 original size:11 final size:11
Alignment explanation
Indices: 5121--5152 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
5111 AAGTTCGTGA
5121 TTGAAGATTTT
1 TTGAAGATTTT
*
5132 TTGAAGATATT
1 TTGAAGATTTT
5143 TTGAAGATTT
1 TTGAAGATTT
5153 GAAGACAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (11 bp):
TTGAAGATTTT
Found at i:9078 original size:28 final size:27
Alignment explanation
Indices: 9043--9144 Score: 168
Period size: 27 Copynumber: 3.7 Consensus size: 27
9033 AAGTGGACTC
*
9043 AAAATGACCAAAATGCCCCTGAATGCG
1 AAAATGACCAAAATGCCCCTGAATGTG
*
9070 AAAAATGACCAAAATACCCCTGAATGTG
1 -AAAATGACCAAAATGCCCCTGAATGTG
9098 AAAATGACCAAAATGCCCCTGAATGTG
1 AAAATGACCAAAATGCCCCTGAATGTG
*
9125 AAAATGATCAAAATGCCCCT
1 AAAATGACCAAAATGCCCCT
9145 AGGTGACCCT
Statistics
Matches: 70, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
27 45 0.64
28 25 0.36
ACGTcount: A:0.43, C:0.24, G:0.16, T:0.18
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGAATGTG
Found at i:9548 original size:91 final size:91
Alignment explanation
Indices: 9400--9707 Score: 367
Period size: 91 Copynumber: 3.4 Consensus size: 91
9390 ACAAATCCAA
* * * * ** * *
9400 CTTTGAAGAAATAATGCACCGCATCC-CCTTGATTCACTGAATCATTATG-ATTTATTTGAAAAT
1 CTTTGAAGAAATAAGGCACCGC--CCAACTTGATTCACCGAATGATCCTGAACTGATTTGAAAAT
*
9463 GTACTGCACCGAGCTCACCGAATTCCGAT
64 CTACTGCACCGAGCTCACCGAA-TCCGAT
*
9492 C-TTGAAGAAATAAGGCACCGCCTCAACTTGATTCTCCGAATGATCCTGAAC-GATTTGAAAATC
1 CTTTGAAGAAATAAGGCACCGCC-CAACTTGATTCACCGAATGATCCTGAACTGATTTGAAAATC
*
9555 TACTGCACCGAGCTCACCGAATCTGA-
65 TACTGCACCGAGCTCACCGAATCCGAT
* *
9581 CTTTGAAGAAGTAAGGCACCGCCCTAACTTGATTCACCGAATGATCTTGAACTG-TTTGAAAATC
1 CTTTGAAGAAATAAGGCACCGCCC-AACTTGATTCACCGAATGATCCTGAACTGATTTGAAAATC
* * *
9645 TATTGCACCGAGCTCACTGAATCCAAT
65 TACTGCACCGAGCTCACCGAATCCGAT
*
9672 CTTTGAAGCAATAAGGCACCGCCCCAACTTGATTCA
1 CTTTGAAGAAATAAGGCACCG-CCCAACTTGATTCA
9708 TCCTTAACTT
Statistics
Matches: 188, Mismatches: 20, Indels: 17
0.84 0.09 0.08
Matches are distributed among these distances:
89 3 0.02
90 82 0.44
91 98 0.52
92 5 0.03
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.27
Consensus pattern (91 bp):
CTTTGAAGAAATAAGGCACCGCCCAACTTGATTCACCGAATGATCCTGAACTGATTTGAAAATCT
ACTGCACCGAGCTCACCGAATCCGAT
Found at i:9621 original size:90 final size:90
Alignment explanation
Indices: 9453--9707 Score: 347
Period size: 90 Copynumber: 2.8 Consensus size: 90
9443 ATTATGATTT
*
9453 ATTTGAAAATGTACTGCACCGAGCTCACCGAATTCCGA-TCTTGAAGAAATAAGGCACCG-CCTC
1 ATTTGAAAATCTACTGCACCGAGCTCACCGAA-TCCGACT-TTGAAG-AATAAGGCACCGCCCT-
*
9516 AACTTGATTCTCCGAATGATCCTGAAC-G
62 AACTTGATTCACCGAATGATCCTGAACTG
*
9544 ATTTGAAAATCTACTGCACCGAGCTCACCGAATCTGACTTTGAAGAAGTAAGGCACCGCCCTAAC
1 ATTTGAAAATCTACTGCACCGAGCTCACCGAATCCGACTTTGAAGAA-TAAGGCACCGCCCTAAC
*
9609 TTGATTCACCGAATGATCTTGAACTG
65 TTGATTCACCGAATGATCCTGAACTG
* * * *
9635 -TTTGAAAATCTATTGCACCGAGCTCACTGAATCCAATCTTTGAAGCAATAAGGCACCGCCCCAA
1 ATTTGAAAATCTACTGCACCGAGCTCACCGAATCCGA-CTTTGAAG-AATAAGGCACCGCCCTAA
9699 CTTGATTCA
64 CTTGATTCA
9708 TCCTTAACTT
Statistics
Matches: 149, Mismatches: 9, Indels: 12
0.88 0.05 0.07
Matches are distributed among these distances:
89 2 0.01
90 77 0.52
91 68 0.46
92 2 0.01
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (90 bp):
ATTTGAAAATCTACTGCACCGAGCTCACCGAATCCGACTTTGAAGAATAAGGCACCGCCCTAACT
TGATTCACCGAATGATCCTGAACTG
Done.