Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008575.1 Corchorus capsularis cultivar CVL-1 contig08596, 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: 28837
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:2705 original size:12 final size:11
Alignment explanation
Indices: 2683--2708 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2673 ATTTTGTAAA
2683 TTTAATTTTTT
1 TTTAATTTTTT
2694 TTTAATTTTTT
1 TTTAATTTTTT
2705 TTTA
1 TTTA
2709 CTAAATTGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTAATTTTTT
Found at i:2842 original size:33 final size:33
Alignment explanation
Indices: 2800--2929 Score: 206
Period size: 33 Copynumber: 3.9 Consensus size: 33
2790 AAATAGCCTT
* *
2800 GCCGCCCTAGTGGGGCGGCTCCGTCGTGGCAGA
1 GCCGCCCTAGTGGGGAGGCTCCGTCGTGGCTGA
2833 GCCGCCCTAGTGGGGAGGCTCCGTCGTGGCTGA
1 GCCGCCCTAGTGGGGAGGCTCCGTCGTGGCTGA
* *
2866 GCCGTCCTAGTGGGGAGGCTCCGTCGTGGTTGA
1 GCCGCCCTAGTGGGGAGGCTCCGTCGTGGCTGA
* *
2899 GCCGTCCTAGTGGGGAGGCTCCGCCGTGGCT
1 GCCGCCCTAGTGGGGAGGCTCCGTCGTGGCT
2930 AAGGGCAAAA
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 91 1.00
ACGTcount: A:0.08, C:0.30, G:0.42, T:0.19
Consensus pattern (33 bp):
GCCGCCCTAGTGGGGAGGCTCCGTCGTGGCTGA
Found at i:4080 original size:38 final size:38
Alignment explanation
Indices: 4029--4108 Score: 160
Period size: 38 Copynumber: 2.1 Consensus size: 38
4019 ACATATTATT
4029 GGATAATTTGAAAATTGGGGTAGGATTGAAAAGAAAGA
1 GGATAATTTGAAAATTGGGGTAGGATTGAAAAGAAAGA
4067 GGATAATTTGAAAATTGGGGTAGGATTGAAAAGAAAGA
1 GGATAATTTGAAAATTGGGGTAGGATTGAAAAGAAAGA
4105 GGAT
1 GGAT
4109 TAGTAAAGGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.24
Consensus pattern (38 bp):
GGATAATTTGAAAATTGGGGTAGGATTGAAAAGAAAGA
Found at i:4695 original size:30 final size:30
Alignment explanation
Indices: 4659--4718 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
4649 TTTATTTAAA
4659 TTGTAATTAGATTTGGGAAAGGGGTTTGTT
1 TTGTAATTAGATTTGGGAAAGGGGTTTGTT
4689 TTGTAATTAGATTTGGGAAAGGGGTTTGTT
1 TTGTAATTAGATTTGGGAAAGGGGTTTGTT
4719 GGCTCATAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.43
Consensus pattern (30 bp):
TTGTAATTAGATTTGGGAAAGGGGTTTGTT
Found at i:6931 original size:24 final size:24
Alignment explanation
Indices: 6899--6946 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
6889 AAACCATCCC
6899 CATTTCCATTTCCATGGTTAAAGG
1 CATTTCCATTTCCATGGTTAAAGG
* *
6923 CATTTCCATTTCCATTGTTTAAGG
1 CATTTCCATTTCCATGGTTAAAGG
6947 AACCAGCAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.42
Consensus pattern (24 bp):
CATTTCCATTTCCATGGTTAAAGG
Found at i:8323 original size:93 final size:93
Alignment explanation
Indices: 8164--8344 Score: 247
Period size: 93 Copynumber: 1.9 Consensus size: 93
8154 GTACTTCAAC
8164 TTTCTTAATATTTTCTATATAATTTTACATGGTGCCCACCCTTACATTGTCCTAGATACCCACCC
1 TTTCTTAATATTTTCTATATAATTTTACATGGTGCCCACCCTTACATTGTCCTAGATACCCACCC
*
8229 TCAATTAATTAACTCGTCAAAATGCCCA
66 TCAATGAATTAACTCGTCAAAATGCCCA
* * ** * ***
8257 TTTCTTAATATTTTGTATGTAATTTTACATGGTGTTCACCCTTA-TTTGGTCCTAGATGTTCACC
1 TTTCTTAATATTTTCTATATAATTTTACATGGTGCCCACCCTTACATT-GTCCTAGATACCCACC
* *
8321 CTCAATGGATTAACTTGTCAAAAT
65 CTCAATGAATTAACTCGTCAAAAT
8345 ATCTTTAAAT
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
92 2 0.03
93 74 0.97
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.40
Consensus pattern (93 bp):
TTTCTTAATATTTTCTATATAATTTTACATGGTGCCCACCCTTACATTGTCCTAGATACCCACCC
TCAATGAATTAACTCGTCAAAATGCCCA
Found at i:10126 original size:10 final size:10
Alignment explanation
Indices: 10097--10127 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
10087 GCATGTTATT
*
10097 TGGCACGAGT
1 TGGCACGAGA
10107 TGGCACGAGA
1 TGGCACGAGA
10117 TGGCACGAGA
1 TGGCACGAGA
10127 T
1 T
10128 TTTCTGACTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.26, C:0.19, G:0.39, T:0.16
Consensus pattern (10 bp):
TGGCACGAGA
Found at i:12509 original size:2 final size:2
Alignment explanation
Indices: 12471--12501 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
12461 TTTTAGTGTA
12471 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12502 TTTATATACT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:17439 original size:62 final size:63
Alignment explanation
Indices: 17326--17494 Score: 259
Period size: 63 Copynumber: 2.6 Consensus size: 63
17316 ATCTATTGAC
17326 ATCTTTTATTTTTCTCCAATTTGATTTTAATTGAACTTAAGAAATTAGATC-TTGGTAGATCTTA
1 ATCTTTTATTTTTCTCCAATTTGATTTT-A---AACTTAAGAAATTAGATCTTTGGTAGATCTTA
17390 AA
62 AA
* *
17392 ATCTTTTTTTTTTCTCCAATTTGATTTTAAACTTAAGAAATTTGATCTTTGGTAGATCTTAAA
1 ATCTTTTATTTTTCTCCAATTTGATTTTAAACTTAAGAAATTAGATCTTTGGTAGATCTTAAA
* *
17455 ATCTTTTAATTTTCTCTAATTTGATTTTAAACTTAAGAAA
1 ATCTTTTATTTTTCTCCAATTTGATTTTAAACTTAAGAAA
17495 GTGGATACCA
Statistics
Matches: 97, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
62 17 0.18
63 52 0.54
65 1 0.01
66 27 0.28
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.49
Consensus pattern (63 bp):
ATCTTTTATTTTTCTCCAATTTGATTTTAAACTTAAGAAATTAGATCTTTGGTAGATCTTAAA
Found at i:19543 original size:48 final size:48
Alignment explanation
Indices: 19488--19587 Score: 191
Period size: 48 Copynumber: 2.1 Consensus size: 48
19478 CATGTATATA
*
19488 TGAGTTGCGTTAAGGGGTTTAATTATCAAAATCAATGTTCCATGAAGT
1 TGAGTTGCGTTAAGCGGTTTAATTATCAAAATCAATGTTCCATGAAGT
19536 TGAGTTGCGTTAAGCGGTTTAATTATCAAAATCAATGTTCCATGAAGT
1 TGAGTTGCGTTAAGCGGTTTAATTATCAAAATCAATGTTCCATGAAGT
19584 TGAG
1 TGAG
19588 GATTTGTAAC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.35
Consensus pattern (48 bp):
TGAGTTGCGTTAAGCGGTTTAATTATCAAAATCAATGTTCCATGAAGT
Found at i:24393 original size:43 final size:46
Alignment explanation
Indices: 24310--24401 Score: 127
Period size: 48 Copynumber: 2.0 Consensus size: 46
24300 AAAAACTATT
*
24310 TTGATTCATGAATGTTATGATTTGCTCTAATCTCATAATATTTTGGTA
1 TTGATTCATGAATGTTATGATTTACTC--ATCTCATAATATTTTGGTA
*
24358 TTGATTCATGAGTGTTATGATTTACTC-T-T-ATAATATTTTGGTA
1 TTGATTCATGAATGTTATGATTTACTCATCTCATAATATTTTGGTA
24401 T
1 T
24402 AAAATTAACG
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
43 15 0.36
44 1 0.02
45 1 0.02
48 25 0.60
ACGTcount: A:0.26, C:0.09, G:0.15, T:0.50
Consensus pattern (46 bp):
TTGATTCATGAATGTTATGATTTACTCATCTCATAATATTTTGGTA
Done.