Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008001.1 Corchorus capsularis cultivar CVL-1 contig08022, 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: 20322
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:3961 original size:2 final size:2
Alignment explanation
Indices: 3954--3980 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3944 ATGGTCAAGA
3954 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3981 GCAAATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9108 original size:2 final size:2
Alignment explanation
Indices: 9103--9135 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
9093 CTTCACTTGA
9103 CT CT CT CT CT CT CT CT CT CT ACT C- CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT -CT CT CT CT CT CT C
9136 GTTTTCTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.03, C:0.52, G:0.00, T:0.45
Consensus pattern (2 bp):
CT
Found at i:10547 original size:30 final size:30
Alignment explanation
Indices: 10511--10570 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
10501 AGCCTTAGAT
*
10511 ATTTTAATTTTATGCAACTTAGTCCCTCAA
1 ATTTTAATTTTATACAACTTAGTCCCTCAA
* *
10541 ATTTTAATTTTATACAATTTAGTCCTTCAA
1 ATTTTAATTTTATACAACTTAGTCCCTCAA
10571 CTTTATTCCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.17, G:0.05, T:0.47
Consensus pattern (30 bp):
ATTTTAATTTTATACAACTTAGTCCCTCAA
Found at i:10711 original size:137 final size:135
Alignment explanation
Indices: 10457--10714 Score: 419
Period size: 136 Copynumber: 1.9 Consensus size: 135
10447 TTTATTATAG
* * *
10457 TTTTTCCAAGATTTAGCCCTTCAACTTTATTTAATTTATATAAAAGCCTTAGATATTTTAATTTT
1 TTTTTCCAAGATTTAGCCATTCAACTTTATTTAATTTACATAAAAGCCTTAGACATTTTAATTTT
10522 ATGCAACTTAGTCCCTCAAATTTTAATTTTATACAATTTAGTCCTTCAACTTTATTCCTTTTATT
66 ATGCAACTTAGTCCCTCAAATTTTAATTTTATACAATTTAGTCCTTCAACTTTATTCCTTTTATT
10587 ATTTC
131 ATTTC
* * *
10592 TTTTT-CAAGATTTAGCCATTCGACTTTATTTTTATTTACATAAAAGCCCTTAGACATTTTCATT
1 TTTTTCCAAGATTTAGCCATTCAACTTTA-TTTAATTTACATAAAAG-CCTTAGACATTTTAATT
*
10656 TTATGCAACTTAGTCTCTCAAATATTTAATTTTATACAATTTAGTCCTTCAACTTTATT
64 TTATGCAACTTAGTCCCTCAAAT-TTTAATTTTATACAATTTAGTCCTTCAACTTTATT
10715 TCTTATTTTT
Statistics
Matches: 113, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
134 21 0.19
135 20 0.18
136 37 0.33
137 35 0.31
ACGTcount: A:0.29, C:0.17, G:0.06, T:0.48
Consensus pattern (135 bp):
TTTTTCCAAGATTTAGCCATTCAACTTTATTTAATTTACATAAAAGCCTTAGACATTTTAATTTT
ATGCAACTTAGTCCCTCAAATTTTAATTTTATACAATTTAGTCCTTCAACTTTATTCCTTTTATT
ATTTC
Found at i:19491 original size:67 final size:64
Alignment explanation
Indices: 19380--19569 Score: 279
Period size: 67 Copynumber: 3.0 Consensus size: 64
19370 AACTACTTGC
19380 AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGACTTAGGCAAAAGTTAGAGCACAAGAAAAAA
1 AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACG-CTTAGGCAAAAGTTAGAGCACAA-AAAAAA
19445 A
64 A
19446 AAATGCTCGCTAAGTTGAAAATCCTGCAAAGGACAGCTTAGGCAAAAGTTAGAGCAC-------A
1 AAA-GCTCGCTAAGTTGAAAATCCTGCAAAGGAC-GCTTAGGCAAAAGTTAGAGCACAAAAAAAA
19504 A
64 A
19505 AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGC-CAAAAAAAAA
1 AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGAC-GCTTAGGCAAAAGTTAGAGCACAAAAAAAAA
19569 A
1 A
19570 CCCCCCAAAG
Statistics
Matches: 114, Mismatches: 1, Indels: 20
0.84 0.01 0.15
Matches are distributed among these distances:
57 1 0.01
58 50 0.44
59 5 0.04
64 3 0.03
66 3 0.03
67 51 0.45
68 1 0.01
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.16
Consensus pattern (64 bp):
AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGCTTAGGCAAAAGTTAGAGCACAAAAAAAAA
Found at i:19543 original size:58 final size:58
Alignment explanation
Indices: 19444--19564 Score: 217
Period size: 58 Copynumber: 2.1 Consensus size: 58
19434 ACAAGAAAAA
19444 AAAAATGCTCGCTAAGTTGAAAATCCTGCAAAGGACAGCTTAGGCAAAAGTTAGAGCAC
1 AAAAATGCTCGCTAAGTTGAAAATCCTGCAAAGGACAGCTTAGGCAAAAGTTAGAGC-C
*
19503 AAAAA-GCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGCC
1 AAAAATGCTCGCTAAGTTGAAAATCCTGCAAAGGACAGCTTAGGCAAAAGTTAGAGCC
19560 AAAAA
1 AAAAA
19565 AAAAACCCCC
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
57 6 0.10
58 50 0.82
59 5 0.08
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.17
Consensus pattern (58 bp):
AAAAATGCTCGCTAAGTTGAAAATCCTGCAAAGGACAGCTTAGGCAAAAGTTAGAGCC
Done.