Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014709.1 Corchorus capsularis cultivar CVL-1 contig14730, 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: 18230
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:573 original size:30 final size:29
Alignment explanation
Indices: 506--577 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
496 ACACCGAACC
****
506 GTCAAATAAGCCCCTGAACTATTATTTCA
1 GTCAAATAAGCCCCTGAACTATTAAAAAA
* *
535 GCCAAATAAGCCCCTGAACTCTTAAAAAA
1 GTCAAATAAGCCCCTGAACTATTAAAAAA
564 TGTCAAATAAGCCC
1 -GTCAAATAAGCCC
578 TGTTGACAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
29 23 0.66
30 12 0.34
ACGTcount: A:0.39, C:0.26, G:0.11, T:0.24
Consensus pattern (29 bp):
GTCAAATAAGCCCCTGAACTATTAAAAAA
Found at i:4372 original size:31 final size:31
Alignment explanation
Indices: 4330--4437 Score: 132
Period size: 31 Copynumber: 3.5 Consensus size: 31
4320 TAGGCTAAAT
4330 GCTCAATTTGGTCCTAAACCTTTGAGCGAGC
1 GCTCAATTTGGTCCTAAACCTTTGAGCGAGC
* * * *
4361 GCTCAAATTGGTCCTAAATCTTTGA--AAAC
1 GCTCAATTTGGTCCTAAACCTTTGAGCGAGC
4390 GCTCAATTTGGTCCTAAACCTTTGAGCG-GTC
1 GCTCAATTTGGTCCTAAACCTTTGAGCGAG-C
**
4421 GCTCAATTCAGTCCTAA
1 GCTCAATTTGGTCCTAA
4438 TTCTGTCGGC
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
29 25 0.39
31 39 0.61
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.31
Consensus pattern (31 bp):
GCTCAATTTGGTCCTAAACCTTTGAGCGAGC
Found at i:4402 original size:29 final size:30
Alignment explanation
Indices: 4330--4414 Score: 118
Period size: 29 Copynumber: 2.8 Consensus size: 30
4320 TAGGCTAAAT
* *
4330 GCTCAATTTGGTCCTAAACCTTTGAGCGAGC
1 GCTCAATTTGGTCCTAAACCTTTGA-CAAAC
* *
4361 GCTCAAATTGGTCCTAAATCTTTGA-AAAC
1 GCTCAATTTGGTCCTAAACCTTTGACAAAC
4390 GCTCAATTTGGTCCTAAACCTTTGA
1 GCTCAATTTGGTCCTAAACCTTTGA
4415 GCGGTCGCTC
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
29 25 0.52
31 23 0.48
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.32
Consensus pattern (30 bp):
GCTCAATTTGGTCCTAAACCTTTGACAAAC
Found at i:7932 original size:31 final size:31
Alignment explanation
Indices: 7833--7932 Score: 134
Period size: 31 Copynumber: 3.3 Consensus size: 31
7823 AATAGGACTG
7833 AATTGAGCGAC-CGCTCAAAGGTTTAGGACCA
1 AATTGAGC-ACTCGCTCAAAGGTTTAGGACCA
* * *
7864 AATTGAGCGCT--TTCAAAAGTTTAGGACCA
1 AATTGAGCACTCGCTCAAAGGTTTAGGACCA
*
7893 ATTTGAGCACTCGCTCAAAGGTTTAGGACCA
1 AATTGAGCACTCGCTCAAAGGTTTAGGACCA
7924 AATTGAGCA
1 AATTGAGCA
7933 TTTAGCCCAA
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
29 25 0.43
30 1 0.02
31 32 0.55
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (31 bp):
AATTGAGCACTCGCTCAAAGGTTTAGGACCA
Found at i:8477 original size:93 final size:93
Alignment explanation
Indices: 8376--8550 Score: 325
Period size: 93 Copynumber: 1.9 Consensus size: 93
8366 TTTGAGTACA
*
8376 AGTCTAACTTTTGTCCAGTTTTTAGTTTGCAATAGATTGAAAACAGTTTGTCTTGTCGGAATGAT
1 AGTCTAACTTTTGTCCAGTTTTTAATTTGCAATAGATTGAAAACAGTTTGTCTTGTCGGAATGAT
8441 TTTTCTTT-TGGATCAGAGGGTGAGTCTG
66 TTTTCTTTCT-GATCAGAGGGTGAGTCTG
8469 AGTCTAACTTTTGTCCAGTTTTTAATTTGCAATAGATTGAAAACAGTTTGTCTTGTCGGAATGAT
1 AGTCTAACTTTTGTCCAGTTTTTAATTTGCAATAGATTGAAAACAGTTTGTCTTGTCGGAATGAT
8534 TTTTCTTTCTGATCAGA
66 TTTTCTTTCTGATCAGA
8551 TAGTGGGTGC
Statistics
Matches: 80, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
93 79 0.99
94 1 0.01
ACGTcount: A:0.24, C:0.13, G:0.21, T:0.43
Consensus pattern (93 bp):
AGTCTAACTTTTGTCCAGTTTTTAATTTGCAATAGATTGAAAACAGTTTGTCTTGTCGGAATGAT
TTTTCTTTCTGATCAGAGGGTGAGTCTG
Found at i:10379 original size:33 final size:35
Alignment explanation
Indices: 10288--10381 Score: 88
Period size: 33 Copynumber: 2.8 Consensus size: 35
10278 CGGCATGCCG
* *
10288 TGGCTAGGCCGTCCCCCTGGGGCGG--CTGAGCCA
1 TGGCCAGGCCGCCCCCCTGGGGCGGCACTGAGCCA
* ** * *
10321 TGGCCATGCCGCCATCCTAGAGCGGCACT-A-CCA
1 TGGCCAGGCCGCCCCCCTGGGGCGGCACTGAGCCA
*
10354 TGGTCAGGCCGCCCCCCTGGGGCGGCAC
1 TGGCCAGGCCGCCCCCCTGGGGCGGCAC
10382 CGACCCAAAA
Statistics
Matches: 46, Mismatches: 13, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
33 43 0.93
34 1 0.02
35 2 0.04
ACGTcount: A:0.13, C:0.39, G:0.34, T:0.14
Consensus pattern (35 bp):
TGGCCAGGCCGCCCCCCTGGGGCGGCACTGAGCCA
Found at i:10512 original size:32 final size:33
Alignment explanation
Indices: 10444--10542 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 33
10434 AAATAGCCTT
*
10444 GCCGCCCTAATGGGGCGGCTCCGCCGTGGCTAA
1 GCCGCCCTAGTGGGGCGGCTCCGCCGTGGCTAA
* *
10477 GCCGTCCTAGTGGGGCGGCT-AGCCGTGGC-AGA
1 GCCGCCCTAGTGGGGCGGCTCCGCCGTGGCTA-A
*
10509 GCCGCCCTAGTGGGGAGGCTCCGCCGTGGCTAA
1 GCCGCCCTAGTGGGGCGGCTCCGCCGTGGCTAA
10542 G
1 G
10543 GGCAAAAGTG
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
31 1 0.02
32 27 0.47
33 28 0.49
34 1 0.02
ACGTcount: A:0.12, C:0.32, G:0.40, T:0.15
Consensus pattern (33 bp):
GCCGCCCTAGTGGGGCGGCTCCGCCGTGGCTAA
Found at i:15543 original size:11 final size:11
Alignment explanation
Indices: 15527--15562 Score: 72
Period size: 11 Copynumber: 3.3 Consensus size: 11
15517 GCTAACTTTA
15527 TTTACTTTTTT
1 TTTACTTTTTT
15538 TTTACTTTTTT
1 TTTACTTTTTT
15549 TTTACTTTTTT
1 TTTACTTTTTT
15560 TTT
1 TTT
15563 GTGTTGTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTACTTTTTT
Found at i:15691 original size:73 final size:73
Alignment explanation
Indices: 15572--15752 Score: 326
Period size: 73 Copynumber: 2.5 Consensus size: 73
15562 TGTGTTGTTT
* *
15572 AGAAACCTTGGGGTTTCAAAGTAGAAACCTTCACCGTTTCAAAAAGTGAGTTTCTGAGATTTTCT
1 AGAAACCCTGGGGTTTCAAAGTAGAAACCTTCACCGTCTCAAAAAGTGAGTTTCTGAGATTTTCT
15637 TCAAAAGC
66 TCAAAAGC
*
15645 AGAAACCCTGGGCTTTCAAAGTAGAAACCTTCACCGTCTCAAAAAGTGAGTTTCTGAGATTTTCT
1 AGAAACCCTGGGGTTTCAAAGTAGAAACCTTCACCGTCTCAAAAAGTGAGTTTCTGAGATTTTCT
15710 TCAAAAGC
66 TCAAAAGC
*
15718 AGAAACCCTGGGGTTTCAAAGTAGAAACATTCACC
1 AGAAACCCTGGGGTTTCAAAGTAGAAACCTTCACC
15753 TGCTCCAGAA
Statistics
Matches: 103, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 103 1.00
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (73 bp):
AGAAACCCTGGGGTTTCAAAGTAGAAACCTTCACCGTCTCAAAAAGTGAGTTTCTGAGATTTTCT
TCAAAAGC
Done.