Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006000.1 Corchorus capsularis cultivar CVL-1 contig06018, 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: 19071
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Found at i:2338 original size:24 final size:24
Alignment explanation
Indices: 2311--2356 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
2301 ATGACCATCT
*
2311 CCAACAAGTCAAAAGGGTGAGCGA
1 CCAACAAGTCAAAAGGGCGAGCGA
2335 CCAACAAGTCAAAAGGGCGAGC
1 CCAACAAGTCAAAAGGGCGAGC
2357 AATTGTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.41, C:0.24, G:0.28, T:0.07
Consensus pattern (24 bp):
CCAACAAGTCAAAAGGGCGAGCGA
Found at i:2525 original size:106 final size:106
Alignment explanation
Indices: 2341--2614 Score: 442
Period size: 106 Copynumber: 2.6 Consensus size: 106
2331 GCGACCAACA
* *
2341 AGTCAAAAGGGCGAGCAATTGTAAA-ATTAGCTCTATACTTGACCTCAAGACCAAAGTTAATTAG
1 AGTCAAAAGGGCGAGCAATCGTAAAGATTAGCTCTATACTTGACCTCAGGACCAAAGTTAATTAG
*
2405 CGAGCGATTGGTTTCACTATCCTCGACCCAATAAAAGCCCG
66 CGAGCGATTGGTTTCACTATCCTCGACCCAATAAAAGCACG
* * *
2446 AGTCAAAAGGGCGAGCAATCGTAAAGATTAGCTCTATACTTGACTTCAGGACCAATGTTAATTGG
1 AGTCAAAAGGGCGAGCAATCGTAAAGATTAGCTCTATACTTGACCTCAGGACCAAAGTTAATTAG
*
2511 CGAGCGATTGGTTTCACTATCCTCGACCTAATAAAAGCACG
66 CGAGCGATTGGTTTCACTATCCTCGACCCAATAAAAGCACG
* * * *
2552 AGTCAAAAGGGCGAGCAATCGTAAAGATTAGCTTTATACTTGACCTCAGAACTAAAGATAATT
1 AGTCAAAAGGGCGAGCAATCGTAAAGATTAGCTCTATACTTGACCTCAGGACCAAAGTTAATT
2615 GGCAAGCAGT
Statistics
Matches: 155, Mismatches: 13, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
105 24 0.15
106 131 0.85
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (106 bp):
AGTCAAAAGGGCGAGCAATCGTAAAGATTAGCTCTATACTTGACCTCAGGACCAAAGTTAATTAG
CGAGCGATTGGTTTCACTATCCTCGACCCAATAAAAGCACG
Found at i:2771 original size:24 final size:24
Alignment explanation
Indices: 2744--2789 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
2734 ATGACCATCT
*
2744 CCAACAAGTCAAAAGGGTGAGCGA
1 CCAACAAGTCAAAAGGGCGAGCGA
2768 CCAACAAGTCAAAAGGGCGAGC
1 CCAACAAGTCAAAAGGGCGAGC
2790 AATTGTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.41, C:0.24, G:0.28, T:0.07
Consensus pattern (24 bp):
CCAACAAGTCAAAAGGGCGAGCGA
Found at i:3172 original size:19 final size:19
Alignment explanation
Indices: 3148--3185 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
3138 GCACCGAATG
3148 CTCCCCTGAA-CACGTGCAA
1 CTCCCCT-AAGCACGTGCAA
3167 CTCCCCTAAGCACGTGCAA
1 CTCCCCTAAGCACGTGCAA
3186 TCACCAATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.26, C:0.42, G:0.16, T:0.16
Consensus pattern (19 bp):
CTCCCCTAAGCACGTGCAA
Found at i:3317 original size:119 final size:119
Alignment explanation
Indices: 3105--3366 Score: 470
Period size: 119 Copynumber: 2.2 Consensus size: 119
3095 CGCATGATCA
* *
3105 CCAACCGCGTGAGTGAAGAATGCTTAATGAAGAGCACCGAATGCTCCCCTGAACACGTGCAACTC
1 CCAACCGCGCGAGTGAAGAATGCTTAACGAAGAGCACCGAATGCTCCCCTGAACACGTGCAACTC
*
3170 CCCTAAGCACGTGCAATCACCAATGCACGAAAGAAGAGTGCTCAATGAAGAGTG
66 CCCTAAGCACGTGCAATCACCAACGCACGAAAGAAGAGTGCTCAATGAAGAGTG
*
3224 CCAACCGCGCGAGTGAAGAATGCTTAACGAAGAGCACCGAATGCTCCCTTGAACACGTGCAACTC
1 CCAACCGCGCGAGTGAAGAATGCTTAACGAAGAGCACCGAATGCTCCCCTGAACACGTGCAACTC
*
3289 CCCTAAGCACGTGCAATCACCAACGCACGAAAGAAGAGTGCTCAATTAAGAGTG
66 CCCTAAGCACGTGCAATCACCAACGCACGAAAGAAGAGTGCTCAATGAAGAGTG
*
3343 CCGACCGCGCGAGTGAAGAATGCT
1 CCAACCGCGCGAGTGAAGAATGCT
3367 AGCACCAGAT
Statistics
Matches: 137, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
119 137 1.00
ACGTcount: A:0.33, C:0.28, G:0.24, T:0.15
Consensus pattern (119 bp):
CCAACCGCGCGAGTGAAGAATGCTTAACGAAGAGCACCGAATGCTCCCCTGAACACGTGCAACTC
CCCTAAGCACGTGCAATCACCAACGCACGAAAGAAGAGTGCTCAATGAAGAGTG
Found at i:5158 original size:19 final size:18
Alignment explanation
Indices: 5129--5170 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
5119 GAGGAATTTT
*
5129 TTAAGTAAAAATATAATA
1 TTAAATAAAAATATAATA
*
5147 TATAAATAAAAATTTAATA
1 T-TAAATAAAAATATAATA
5166 TTAAA
1 TTAAA
5171 ACAATTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
TTAAATAAAAATATAATA
Found at i:5500 original size:86 final size:86
Alignment explanation
Indices: 5404--5575 Score: 344
Period size: 86 Copynumber: 2.0 Consensus size: 86
5394 CTTTCTAATC
5404 TCTTATTAATTTCCTTATTTTCATTATCTAATGCAACTCTAGCTAAATCTAATCTGTAAGATTAG
1 TCTTATTAATTTCCTTATTTTCATTATCTAATGCAACTCTAGCTAAATCTAATCTGTAAGATTAG
5469 TCAGTCTTGTTTGTGGGTAAA
66 TCAGTCTTGTTTGTGGGTAAA
5490 TCTTATTAATTTCCTTATTTTCATTATCTAATGCAACTCTAGCTAAATCTAATCTGTAAGATTAG
1 TCTTATTAATTTCCTTATTTTCATTATCTAATGCAACTCTAGCTAAATCTAATCTGTAAGATTAG
5555 TCAGTCTTGTTTGTGGGTAAA
66 TCAGTCTTGTTTGTGGGTAAA
5576 AGTACAAAAT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 86 1.00
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (86 bp):
TCTTATTAATTTCCTTATTTTCATTATCTAATGCAACTCTAGCTAAATCTAATCTGTAAGATTAG
TCAGTCTTGTTTGTGGGTAAA
Found at i:5797 original size:12 final size:12
Alignment explanation
Indices: 5780--5813 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
5770 CATTTTTCAG
5780 AATAAAAAATAA
1 AATAAAAAATAA
*
5792 AATAAAAAATAG
1 AATAAAAAATAA
5804 AA-AAAAAATA
1 AATAAAAAATA
5814 TTTTCTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 8 0.38
12 13 0.62
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (12 bp):
AATAAAAAATAA
Found at i:9128 original size:88 final size:88
Alignment explanation
Indices: 9029--9199 Score: 324
Period size: 88 Copynumber: 1.9 Consensus size: 88
9019 TGGGATTCTT
9029 AAATTATTATGAACTTTAATTTTACATTATCTTCTCCAATGATTCCGGATTTTATTTCAAATATT
1 AAATTATTATGAACTTTAATTTTACATTATCTTCTCCAATGATTCCGGATTTTATTTCAAATATT
*
9094 TTGGGCTCTGTAGTGTGTGTGGC
66 TTGGACTCTGTAGTGTGTGTGGC
*
9117 AAATTATTATGAACTTTAATTTTACATTATCTTCTCCAATGATTCTGGATTTTATTTCAAATATT
1 AAATTATTATGAACTTTAATTTTACATTATCTTCTCCAATGATTCCGGATTTTATTTCAAATATT
9182 TTGGACTCTGTAGTGTGT
66 TTGGACTCTGTAGTGTGT
9200 TTTGCCTGTC
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 81 1.00
ACGTcount: A:0.26, C:0.13, G:0.14, T:0.47
Consensus pattern (88 bp):
AAATTATTATGAACTTTAATTTTACATTATCTTCTCCAATGATTCCGGATTTTATTTCAAATATT
TTGGACTCTGTAGTGTGTGTGGC
Done.