Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015963.1 Corchorus capsularis cultivar CVL-1 contig15984, 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: 9842
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Found at i:2544 original size:8 final size:8
Alignment explanation
Indices: 2516--2549 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
2506 GAATCGGCTA
2516 TGAATTTT
1 TGAATTTT
*
2524 TGAAGTTTC
1 TGAA-TTTT
2533 TGAATTTT
1 TGAATTTT
2541 TGAATTTT
1 TGAATTTT
2549 T
1 T
2550 CAAGAAGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:3554 original size:33 final size:34
Alignment explanation
Indices: 3517--3590 Score: 91
Period size: 33 Copynumber: 2.2 Consensus size: 34
3507 CGCCTAGCGA
* *
3517 TGGCCGGTTG-TGGCCGGACATGTCC-ATGTCGCG
1 TGGCCGGTTGTTGGCCGGACATCTCCGA-GTCACG
*
3550 TGGCCGG-TGTTGGCCGGGCATCTCCGAGTCACG
1 TGGCCGGTTGTTGGCCGGACATCTCCGAGTCACG
3583 TGGCCGGT
1 TGGCCGGT
3591 CTTCTCCAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
32 2 0.06
33 32 0.91
34 1 0.03
ACGTcount: A:0.08, C:0.28, G:0.41, T:0.23
Consensus pattern (34 bp):
TGGCCGGTTGTTGGCCGGACATCTCCGAGTCACG
Found at i:3609 original size:23 final size:23
Alignment explanation
Indices: 3560--3615 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
3550 TGGCCGGTGT
* * *
3560 TGGCCGGGCATCTCCGAGTCACG
1 TGGCCGGTCATCTCCAAGTCACA
* *
3583 TGGCCGGTCTTCTCCAAGTCGCA
1 TGGCCGGTCATCTCCAAGTCACA
*
3606 TGGCAGGTCA
1 TGGCCGGTCA
3616 CTCGCGCCTC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.14, C:0.32, G:0.32, T:0.21
Consensus pattern (23 bp):
TGGCCGGTCATCTCCAAGTCACA
Found at i:4828 original size:114 final size:113
Alignment explanation
Indices: 4619--5164 Score: 790
Period size: 114 Copynumber: 4.8 Consensus size: 113
4609 GAGAATCAAA
* * * * * * * *
4619 ACGCCGTTAAATGGAGGCGTCTGAACCTCAAAATGCCGCCATCTTTGATTTTTCTCCGAGAAAGA
1 ACGCCGCTAAATGGAGGCGTCTGAACCACAAAACGCCGCGATCTTTAATTTTTCTTCGAGGAAGG
* * *
4684 C-AATTTGGTAAAAAAGAAGGCTAAAAGATAGCGGCGTCTTGACCCCAG
66 CAAATTGGGT-AAAATGAAGGCTAAAAGATAGCGGCGTCTTGACACCAG
* * *
4732 ACGCCGCTAAATGGAGACGTCTGAACCACAAAACACCGCGATATTTAATTTTTCTTCGAGGAAGG
1 ACGCCGCTAAATGGAGGCGTCTGAACCACAAAACGCCGCGATCTTTAATTTTTCTTCGAGGAAGG
*
4797 CAAATTGGGTAAAATTGAAGGCTAAAAGATAGCGGCGTCTTAACACCAG
66 CAAATTGGGTAAAA-TGAAGGCTAAAAGATAGCGGCGTCTTGACACCAG
* * *
4846 ACGCCGCTAAATGGAGGTGTCTGAACCACAAAACACCGCGATCTTTAATTTTTCTTCGATGAAGG
1 ACGCCGCTAAATGGAGGCGTCTGAACCACAAAACGCCGCGATCTTTAATTTTTCTTCGAGGAAGG
4911 CAAATTGGGTAAAATTGAAGGCTAAAAGATAGCGGCGTCTTGACACCAG
66 CAAATTGGGTAAAA-TGAAGGCTAAAAGATAGCGGCGTCTTGACACCAG
* * *
4960 ACGCTGCTAAATGGAGGCGTCTGAATCACAAAACGCCGCGATCTTTATTTTTTC-TCTGAGGAAG
1 ACGCCGCTAAATGGAGGCGTCTGAACCACAAAACGCCGCGATCTTTAATTTTTCTTC-GAGGAAG
* * *
5024 GCAAATTGGGTAAAAAGAAGGCTAAAAGATAGCGGCATCTTGACCCCAG
65 GCAAATTGGGTAAAATGAAGGCTAAAAGATAGCGGCGTCTTGACACCAG
* *
5073 ACGCTGCTAAATGGAGGCGTCTGAACCACAAAACGCCGCGATCTTTAAGTTTTTTTTCGAGGAAG
1 ACGCCGCTAAATGGAGGCGTCTGAACCACAAAACGCCGCGATCTTTAA-TTTTTCTTCGAGGAAG
*
5138 GCAAATTGGGTAAAATGAAGCCTAAAA
65 GCAAATTGGGTAAAATGAAGGCTAAAA
5165 ATATAAATAC
Statistics
Matches: 394, Mismatches: 34, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
113 138 0.35
114 254 0.64
115 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (113 bp):
ACGCCGCTAAATGGAGGCGTCTGAACCACAAAACGCCGCGATCTTTAATTTTTCTTCGAGGAAGG
CAAATTGGGTAAAATGAAGGCTAAAAGATAGCGGCGTCTTGACACCAG
Found at i:5114 original size:227 final size:226
Alignment explanation
Indices: 4619--5164 Score: 783
Period size: 227 Copynumber: 2.4 Consensus size: 226
4609 GAGAATCAAA
* * * * * * *
4619 ACGCCGTTAAATGGAGGCGTCTGAACCTCAAAATGCCGCCATCTTTGATTTTTCTCCGAGAAAG-
1 ACGCCGCTAAATGGAGGCGTCTGAACCACAAAACGCCGCGATCTTTAATTTTTCTTCGAGAAGGC
* * *
4683 ACAATTTGGTAAAAAAGAAGGCTAAAAGATAGCGGCGTCTTGACCCCAGACGCCGCTAAATGGAG
66 A-AATTGGGT-AAAATGAAGGCTAAAAGATAGCGGCGTCTTGACACCAGACGCCGCTAAATGGAG
*
4748 ACGTCTGAACCACAAAACACCGCGATATTTAATTTTTCTTCGAGGAAGGCAAATTGGGTAAAATT
129 ACGTCTGAACCACAAAACACCGCGATATTTAATTTTTCTTCGAGGAAGGCAAATTGGGTAAAATA
*
4813 GAAGGCTAAAAGATAGCGGCGTCTTAACACCAG
194 GAAGGCTAAAAGATAGCGGCATCTTAACACCAG
* *
4846 ACGCCGCTAAATGGAGGTGTCTGAACCACAAAACACCGCGATCTTTAATTTTTCTTCGATGAAGG
1 ACGCCGCTAAATGGAGGCGTCTGAACCACAAAACGCCGCGATCTTTAATTTTTCTTCGA-GAAGG
*
4911 CAAATTGGGTAAAATTGAAGGCTAAAAGATAGCGGCGTCTTGACACCAGACGCTGCTAAATGGAG
65 CAAATTGGGTAAAA-TGAAGGCTAAAAGATAGCGGCGTCTTGACACCAGACGCCGCTAAATGGAG
* * * * *
4976 GCGTCTGAATCACAAAACGCCGCGATCTTTATTTTTTC-TCTGAGGAAGGCAAATTGGGTAAAA-
129 ACGTCTGAACCACAAAACACCGCGATATTTAATTTTTCTTC-GAGGAAGGCAAATTGGGTAAAAT
* *
5039 AGAAGGCTAAAAGATAGCGGCATCTTGACCCCAG
193 AGAAGGCTAAAAGATAGCGGCATCTTAACACCAG
* *
5073 ACGCTGCTAAATGGAGGCGTCTGAACCACAAAACGCCGCGATCTTTAAGTTTTTTTTCGAGGAAG
1 ACGCCGCTAAATGGAGGCGTCTGAACCACAAAACGCCGCGATCTTTAA-TTTTTCTTCGA-GAAG
*
5138 GCAAATTGGGTAAAATGAAGCCTAAAA
64 GCAAATTGGGTAAAATGAAGGCTAAAA
5165 ATATAAATAC
Statistics
Matches: 286, Mismatches: 28, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
227 143 0.50
228 142 0.50
229 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (226 bp):
ACGCCGCTAAATGGAGGCGTCTGAACCACAAAACGCCGCGATCTTTAATTTTTCTTCGAGAAGGC
AAATTGGGTAAAATGAAGGCTAAAAGATAGCGGCGTCTTGACACCAGACGCCGCTAAATGGAGAC
GTCTGAACCACAAAACACCGCGATATTTAATTTTTCTTCGAGGAAGGCAAATTGGGTAAAATAGA
AGGCTAAAAGATAGCGGCATCTTAACACCAG
Found at i:9428 original size:12 final size:12
Alignment explanation
Indices: 9411--9438 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
9401 CAACTGACGT
9411 TAATTGATTTAC
1 TAATTGATTTAC
9423 TAATTGATTTAC
1 TAATTGATTTAC
9435 TAAT
1 TAAT
9439 AGAGGCATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (12 bp):
TAATTGATTTAC
Done.