Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006016.1 Corchorus capsularis cultivar CVL-1 contig06034, 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: 26200
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:540 original size:84 final size:84
Alignment explanation
Indices: 399--565 Score: 325
Period size: 84 Copynumber: 2.0 Consensus size: 84
389 GACTTCCGGT
*
399 CCGATTACTTTCACTAGCTTATCTCTTAAAACATGAAATTAGCTCCTAACAAGTTTATATATGCT
1 CCGATTACTTTCACTAGCCTATCTCTTAAAACATGAAATTAGCTCCTAACAAGTTTATATATGCT
464 TAATTAAAACAAACAAAAA
66 TAATTAAAACAAACAAAAA
483 CCGATTACTTTCACTAGCCTATCTCTTAAAACATGAAATTAGCTCCTAACAAGTTTATATATGCT
1 CCGATTACTTTCACTAGCCTATCTCTTAAAACATGAAATTAGCTCCTAACAAGTTTATATATGCT
548 TAATTAAAACAAACAAAA
66 TAATTAAAACAAACAAAA
566 GAAAATTATA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 82 1.00
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.32
Consensus pattern (84 bp):
CCGATTACTTTCACTAGCCTATCTCTTAAAACATGAAATTAGCTCCTAACAAGTTTATATATGCT
TAATTAAAACAAACAAAAA
Found at i:2119 original size:25 final size:25
Alignment explanation
Indices: 2074--2122 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2064 TTTTGAACTC
*
2074 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
2099 ATTATTTACTTA-ATAATATATATT
1 ATTATTTA-TTATATAAAATATATT
2123 ATATCTAGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:2460 original size:12 final size:12
Alignment explanation
Indices: 2443--2477 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
2433 TTCTGTTGAT
2443 AATATTCTCTAG
1 AATATTCTCTAG
*
2455 AATATTCTCTGG
1 AATATTCTCTAG
2467 AATATTCTCTA
1 AATATTCTCTA
2478 TATCTCTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.31, C:0.17, G:0.09, T:0.43
Consensus pattern (12 bp):
AATATTCTCTAG
Found at i:6311 original size:40 final size:41
Alignment explanation
Indices: 6261--6430 Score: 220
Period size: 40 Copynumber: 4.2 Consensus size: 41
6251 ATGTCAACAT
* *
6261 TAATTATAATTTACCAGAGTGAC-ACTTCTGGTGTCAAAGG
1 TAATTTTAATTTACCAAAGTGACAACTTCTGGTGTCAAAGG
* *
6301 TAATTTTAATTTA-CAAAGTGACAACTTATGGTGTCAAAAG
1 TAATTTTAATTTACCAAAGTGACAACTTCTGGTGTCAAAGG
* * ** *
6341 TAATTTCAATTTACCAAGGGTGACAACTTCTAATGTCAGCA-G
1 TAATTTTAATTTACCAA-AGTGACAACTTCTGGTGTCA-AAGG
6383 TAATTTTAATTTACCAAAGTGACAACTTCTGGTGTCAAAGG
1 TAATTTTAATTTACCAAAGTGACAACTTCTGGTGTCAAAGG
6424 TAATTTT
1 TAATTTT
6431 CAATATTATT
Statistics
Matches: 110, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 40 0.36
41 28 0.25
42 33 0.30
43 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (41 bp):
TAATTTTAATTTACCAAAGTGACAACTTCTGGTGTCAAAGG
Found at i:6378 original size:42 final size:41
Alignment explanation
Indices: 6268--6434 Score: 203
Period size: 42 Copynumber: 4.1 Consensus size: 41
6258 CATTAATTAT
* * *
6268 AATTTACCAGAGTGAC-ACTTCTGGTGTCAAAGGTAATTTT
1 AATTTACCAAAGTGACAACTTCTGGTGTCAAAAGTAATTTC
*
6308 AATTTA-CAAAGTGACAACTTATGGTGTCAAAAGTAATTTC
1 AATTTACCAAAGTGACAACTTCTGGTGTCAAAAGTAATTTC
* ** ** *
6348 AATTTACCAAGGGTGACAACTTCTAATGTCAGCAGTAATTTT
1 AATTTACCAA-AGTGACAACTTCTGGTGTCAAAAGTAATTTC
*
6390 AATTTACCAAAGTGACAACTTCTGGTGTCAAAGGTAATTTTC
1 AATTTACCAAAGTGACAACTTCTGGTGTCAAAAGTAA-TTTC
6432 AAT
1 AAT
6435 ATTATTTACT
Statistics
Matches: 105, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
39 8 0.08
40 33 0.31
41 24 0.23
42 40 0.38
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34
Consensus pattern (41 bp):
AATTTACCAAAGTGACAACTTCTGGTGTCAAAAGTAATTTC
Found at i:6970 original size:28 final size:29
Alignment explanation
Indices: 6937--6998 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
6927 TTTTTCAAAA
6937 AATAATCGACGGG-AAAAAAAACAAAATC
1 AATAATCGACGGGAAAAAAAAACAAAATC
6965 AATAATCGACGGGAAAAAAAAACAAAATC
1 AATAATCGACGGGAAAAAAAAACAAAATC
6994 AATAA
1 AATAA
6999 ATGCAACACT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 13 0.39
29 20 0.61
ACGTcount: A:0.63, C:0.13, G:0.13, T:0.11
Consensus pattern (29 bp):
AATAATCGACGGGAAAAAAAAACAAAATC
Found at i:8430 original size:2 final size:2
Alignment explanation
Indices: 8425--8454 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
8415 TCTCTCTCTC
8425 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8455 AAGAAGAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11531 original size:23 final size:22
Alignment explanation
Indices: 11505--11555 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
11495 AATGCTGTGA
*
11505 TAAAACCTTTCTATTTTTGTTTT
1 TAAAACCTTT-TATTTTTGCTTT
**
11528 TAAAGTCTTTTATTTTTGCTTT
1 TAAAACCTTTTATTTTTGCTTT
*
11550 CAAAAC
1 TAAAAC
11556 TTCCATTTTG
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.25, C:0.14, G:0.06, T:0.55
Consensus pattern (22 bp):
TAAAACCTTTTATTTTTGCTTT
Found at i:18724 original size:14 final size:15
Alignment explanation
Indices: 18707--18739 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
18697 GAAAACAGGG
*
18707 ATTATGAA-ATAACA
1 ATTATGAAGAAAACA
18721 ATTATGAAGAAAACA
1 ATTATGAAGAAAACA
18736 ATTA
1 ATTA
18740 AACTAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.58, C:0.06, G:0.09, T:0.27
Consensus pattern (15 bp):
ATTATGAAGAAAACA
Found at i:18769 original size:6 final size:6
Alignment explanation
Indices: 18760--18792 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
18750 AAAGCAAAGC
18760 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
18793 GCAGATTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:18804 original size:12 final size:13
Alignment explanation
Indices: 18789--18833 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
18779 AATCTAAATC
18789 TAAAGCAGATT-A
1 TAAAGCAGATTAA
*
18801 TAAAGCAAATTAA
1 TAAAGCAGATTAA
18814 TAAAGCAGATTAA
1 TAAAGCAGATTAA
18827 TAAAGCA
1 TAAAGCA
18834 AACAATAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22
Consensus pattern (13 bp):
TAAAGCAGATTAA
Found at i:18840 original size:25 final size:25
Alignment explanation
Indices: 18789--18841 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
18779 AATCTAAATC
*
18789 TAAAGCAGATTATAAAGCAAATTAA
1 TAAAGCAGATTATAAAGCAAATCAA
18814 TAAAGCAGATTAATAAAGCAAA-CAA
1 TAAAGCAGATT-ATAAAGCAAATCAA
18839 TAA
1 TAA
18842 TTAAAAAGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.58, C:0.09, G:0.11, T:0.21
Consensus pattern (25 bp):
TAAAGCAGATTATAAAGCAAATCAA
Found at i:20039 original size:13 final size:13
Alignment explanation
Indices: 20021--20047 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
20011 CCAATTATAG
20021 GTTTATATGGGCT
1 GTTTATATGGGCT
20034 GTTTATATGGGCT
1 GTTTATATGGGCT
20047 G
1 G
20048 AGTATATTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.07, G:0.33, T:0.44
Consensus pattern (13 bp):
GTTTATATGGGCT
Found at i:25938 original size:13 final size:12
Alignment explanation
Indices: 25904--25942 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
25894 TCTAAATCTT
*
25904 AAATCTAAAGCA
1 AAATATAAAGCA
25916 AAATATAAAGCA
1 AAATATAAAGCA
*
25928 AATTAATAAAGCA
1 AAAT-ATAAAGCA
25941 AA
1 AA
25943 CAATAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.64, C:0.10, G:0.08, T:0.18
Consensus pattern (12 bp):
AAATATAAAGCA
Done.