Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012390.1 Corchorus capsularis cultivar CVL-1 contig12411, 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: 34489
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:6797 original size:27 final size:27
Alignment explanation
Indices: 6767--6823 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
6757 TGTCATTTTA
*
6767 GTCAAATTTTTTTGTTTCA-TAATATTT
1 GTCAAATTTTTTTG-GTCAGTAATATTT
*
6794 GTC-ACTTTTTTTGGTCAGTAATATTT
1 GTCAAATTTTTTTGGTCAGTAATATTT
6820 GTCA
1 GTCA
6824 CTTTAAGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 3 0.12
26 20 0.77
27 3 0.12
ACGTcount: A:0.23, C:0.11, G:0.12, T:0.54
Consensus pattern (27 bp):
GTCAAATTTTTTTGGTCAGTAATATTT
Found at i:6815 original size:26 final size:26
Alignment explanation
Indices: 6773--6827 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 26
6763 TTTAGTCAAA
*
6773 TTTTTTTGTTTCATAATATTTGTCAC
1 TTTTTTTGTGTCATAATATTTGTCAC
6799 TTTTTTTG-GTCAGTAATATTTGTCAC
1 TTTTTTTGTGTCA-TAATATTTGTCAC
6825 TTT
1 TTT
6828 AAGATACCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 3 0.11
26 24 0.89
ACGTcount: A:0.18, C:0.11, G:0.11, T:0.60
Consensus pattern (26 bp):
TTTTTTTGTGTCATAATATTTGTCAC
Found at i:11765 original size:16 final size:16
Alignment explanation
Indices: 11744--11816 Score: 92
Period size: 16 Copynumber: 4.6 Consensus size: 16
11734 AATTTTCGGA
*
11744 TTCGGGTTTGAGCTTT
1 TTCGGGTTCGAGCTTT
* *
11760 TTCGGGTTCGGGTTTT
1 TTCGGGTTCGAGCTTT
*
11776 TTCGGGTTTGAGCTTT
1 TTCGGGTTCGAGCTTT
* *
11792 TTCGGGTTCGGGTTTT
1 TTCGGGTTCGAGCTTT
11808 TTCGGGTTC
1 TTCGGGTTC
11817 AGGTTCAGGC
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.03, C:0.14, G:0.34, T:0.49
Consensus pattern (16 bp):
TTCGGGTTCGAGCTTT
Found at i:11780 original size:32 final size:32
Alignment explanation
Indices: 11744--11815 Score: 144
Period size: 32 Copynumber: 2.2 Consensus size: 32
11734 AATTTTCGGA
11744 TTCGGGTTTGAGCTTTTTCGGGTTCGGGTTTT
1 TTCGGGTTTGAGCTTTTTCGGGTTCGGGTTTT
11776 TTCGGGTTTGAGCTTTTTCGGGTTCGGGTTTT
1 TTCGGGTTTGAGCTTTTTCGGGTTCGGGTTTT
11808 TTCGGGTT
1 TTCGGGTT
11816 CAGGTTCAGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.03, C:0.12, G:0.35, T:0.50
Consensus pattern (32 bp):
TTCGGGTTTGAGCTTTTTCGGGTTCGGGTTTT
Found at i:11821 original size:16 final size:16
Alignment explanation
Indices: 11757--11821 Score: 94
Period size: 16 Copynumber: 4.1 Consensus size: 16
11747 GGGTTTGAGC
11757 TTTTTCGGGTTCGGGT
1 TTTTTCGGGTTCGGGT
* * *
11773 TTTTTCGGGTTTGAGC
1 TTTTTCGGGTTCGGGT
11789 TTTTTCGGGTTCGGGT
1 TTTTTCGGGTTCGGGT
*
11805 TTTTTCGGGTTCAGGT
1 TTTTTCGGGTTCGGGT
11821 T
1 T
11822 CAGGCGGGTT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.03, C:0.12, G:0.34, T:0.51
Consensus pattern (16 bp):
TTTTTCGGGTTCGGGT
Found at i:11830 original size:32 final size:32
Alignment explanation
Indices: 11744--11833 Score: 83
Period size: 32 Copynumber: 2.8 Consensus size: 32
11734 AATTTTCGGA
* ***
11744 TTCGGGTTTGAGCTTTTTCGGGTTCGGGTTTT
1 TTCGGGTTTCAGCTTAGGCGGGTTCGGGTTTT
* ***
11776 TTCGGGTTTGAGCTTTTTCGGGTTCGGGTTTT
1 TTCGGGTTTCAGCTTAGGCGGGTTCGGGTTTT
*
11808 TTCGGG-TTCAGGTTCAGGCGGGTTCG
1 TTCGGGTTTCAGCTT-AGGCGGGTTCG
11834 AATAATTGAC
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
31 6 0.12
32 46 0.88
ACGTcount: A:0.04, C:0.14, G:0.37, T:0.44
Consensus pattern (32 bp):
TTCGGGTTTCAGCTTAGGCGGGTTCGGGTTTT
Found at i:15011 original size:11 final size:11
Alignment explanation
Indices: 14995--15024 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
14985 TCTTGACATA
*
14995 TAATAATAAAT
1 TAATAAGAAAT
15006 TAATAAGAAAT
1 TAATAAGAAAT
15017 TAATAAGA
1 TAATAAGA
15025 TTAATTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (11 bp):
TAATAAGAAAT
Found at i:25618 original size:13 final size:13
Alignment explanation
Indices: 25600--25624 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25590 TCAATGTTTC
25600 TAAATATTATTTA
1 TAAATATTATTTA
25613 TAAATATTATTT
1 TAAATATTATTT
25625 GGAATTCCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATATTATTTA
Found at i:25828 original size:3 final size:3
Alignment explanation
Indices: 25820--25863 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
25810 CGCGTCTGGT
25820 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
25864 TCAAAAGTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28618 original size:23 final size:21
Alignment explanation
Indices: 28568--28619 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
28558 TGTGAACAAT
*
28568 ATATAAGTGAACCAAAAATAT
1 ATATAAGTGAACCAAAAATAC
*
28589 GTCATAAGTGAACCAAAAATCAAC
1 AT-ATAAGTGAACCAAAAAT--AC
28613 ATATAAG
1 ATATAAG
28620 AAAGAAGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 1 0.04
22 17 0.68
23 5 0.20
24 2 0.08
ACGTcount: A:0.54, C:0.13, G:0.12, T:0.21
Consensus pattern (21 bp):
ATATAAGTGAACCAAAAATAC
Found at i:29418 original size:89 final size:88
Alignment explanation
Indices: 29255--29419 Score: 199
Period size: 90 Copynumber: 1.9 Consensus size: 88
29245 TATCACTTAG
* *
29255 CCCTTCAATTTAATTCTTTTCATAAAAATGCACTCAGACACTTTCTTCAATGCAATTTAGTACTC
1 CCCTTCAATTTAATTCTTTTCATAAAAATGCACTCAAACACTTTATTCAATGCAATTTAGTA-TC
*
29320 TCAATTATTTTTTATACGATTTAA
65 TCAAGTATTTTTTATACGATTTAA
* * * * *
29344 CCCTTCAACTTTTATTTTTTTCATAGAAA-GCACTCAAACATTTGTATTCCATGCAATTTAGT-T
1 CCCTTCAA-TTTAATTCTTTTCATAAAAATGCACTCAAACACTT-TATTCAATGCAATTTAGTAT
*
29407 CATCCAGTATTTT
64 C-TCAAGTATTTT
29420 ACTATATACA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
88 2 0.03
89 29 0.45
90 33 0.52
ACGTcount: A:0.30, C:0.21, G:0.07, T:0.43
Consensus pattern (88 bp):
CCCTTCAATTTAATTCTTTTCATAAAAATGCACTCAAACACTTTATTCAATGCAATTTAGTATCT
CAAGTATTTTTTATACGATTTAA
Found at i:31484 original size:2 final size:2
Alignment explanation
Indices: 31477--31513 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
31467 CTAACAGAAG
31477 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31514 TAATCGATGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.