Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013367.1 Corchorus olitorius cultivar O-4 contig13400, 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: 17372
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:480 original size:33 final size:33
Alignment explanation
Indices: 437--499 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
427 GCAAGGATCG
*
437 TATCCTTTTACTCTGTTTGCGACGTCTCCTGCA
1 TATCCCTTTACTCTGTTTGCGACGTCTCCTGCA
470 TATCCCTTTACTCTGTTTGCGACGTCTCCT
1 TATCCCTTTACTCTGTTTGCGACGTCTCCT
500 CCATCGCAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.11, C:0.32, G:0.14, T:0.43
Consensus pattern (33 bp):
TATCCCTTTACTCTGTTTGCGACGTCTCCTGCA
Found at i:1720 original size:2 final size:2
Alignment explanation
Indices: 1709--1741 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1699 TTTTAGTCTG
1709 TA TA -A 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 TA TA
1742 AAAGTATGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3442 original size:22 final size:23
Alignment explanation
Indices: 3367--3421 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
3357 ATGTTACAAG
*
3367 ATTTCATAGGAAGGTTTATTAAA
1 ATTTCATAGGAAGGTTTATAAAA
3390 ATTTCATAGGAAGGTTTATAAAA
1 ATTTCATAGGAAGGTTTATAAAA
3413 ATTTCATAG
1 ATTTCATAG
3422 TTAGGTTATC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.38
Consensus pattern (23 bp):
ATTTCATAGGAAGGTTTATAAAA
Found at i:3587 original size:19 final size:15
Alignment explanation
Indices: 3547--3578 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
3537 TGCTGGGAAT
3547 ATAGTTAGATAGATA
1 ATAGTTAGATAGATA
3562 ATAGTTAGATAGATA
1 ATAGTTAGATAGATA
3577 AT
1 AT
3579 TATTAGTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.34
Consensus pattern (15 bp):
ATAGTTAGATAGATA
Found at i:8061 original size:30 final size:30
Alignment explanation
Indices: 8013--8127 Score: 144
Period size: 30 Copynumber: 3.8 Consensus size: 30
8003 CAAAAAGTGA
8013 CACGTGTACAAAAAAAGTGACACGTGTCACGC
1 CACGTGTAC--AAAAAGTGACACGTGTCACGC
* *
8045 CACGTGTACTAAAAGTGACACGTGTCACCC
1 CACGTGTACAAAAAGTGACACGTGTCACGC
* *
8075 CACGTGTACCAAAAA-TGACACGTGGCATGC
1 CACGTGTA-CAAAAAGTGACACGTGTCACGC
*
8105 CACGTGCACAAAAAG-GACACGTG
1 CACGTGTACAAAAAGTGACACGTG
8128 CCACATGTCA
Statistics
Matches: 74, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
29 14 0.19
30 46 0.62
31 5 0.07
32 9 0.12
ACGTcount: A:0.35, C:0.27, G:0.23, T:0.16
Consensus pattern (30 bp):
CACGTGTACAAAAAGTGACACGTGTCACGC
Found at i:8067 original size:50 final size:48
Alignment explanation
Indices: 7976--8069 Score: 127
Period size: 50 Copynumber: 1.9 Consensus size: 48
7966 CACATGTACC
* *
7976 AAAAAGTGACACGCACGCCATGTTTACCAAAAAGTGACACGTGTACAA
1 AAAAAGTGACACGCACGCCACGTGTACCAAAAAGTGACACGTGTACAA
*
8024 AAAAAGTGACACGTGTCACGCCACGTGTA-CTAAAAGTGACACGTGT
1 AAAAAGTGACAC--G-CACGCCACGTGTACCAAAAAGTGACACGTGT
8070 CACCCCACGT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
48 12 0.30
50 17 0.43
51 11 0.28
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.18
Consensus pattern (48 bp):
AAAAAGTGACACGCACGCCACGTGTACCAAAAAGTGACACGTGTACAA
Found at i:8108 original size:60 final size:61
Alignment explanation
Indices: 8013--8127 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 61
8003 CAAAAAGTGA
* * *
8013 CACGTGTACAAAAAAAGTGACACGTGTCACGCCACGTGTACTAAAAGTGACACGTGTCACCC
1 CACGTGTACAAAAAAAGTGACACGTGGCACGCCACGTGCACAAAAAG-GACACGTGTCACCC
* *
8075 CACGTGTAC-CAAAAA-TGACACGTGGCATGCCACGTGCACAAAAAGGACACGTG
1 CACGTGTACAAAAAAAGTGACACGTGGCACGCCACGTGCACAAAAAGGACACGTG
8128 CCACATGTCA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 8 0.17
60 26 0.54
61 5 0.10
62 9 0.19
ACGTcount: A:0.35, C:0.27, G:0.23, T:0.16
Consensus pattern (61 bp):
CACGTGTACAAAAAAAGTGACACGTGGCACGCCACGTGCACAAAAAGGACACGTGTCACCC
Found at i:8643 original size:22 final size:23
Alignment explanation
Indices: 8618--8665 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
8608 CCACAAATTA
8618 TCCAAC-AATAAGT-CAATAACAG
1 TCCAACAAATAA-TCCAATAACAG
*
8640 TCC-ACAAATTATCCAATAACAG
1 TCCAACAAATAATCCAATAACAG
8662 TCCA
1 TCCA
8666 CAACAATACA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.46, C:0.27, G:0.06, T:0.21
Consensus pattern (23 bp):
TCCAACAAATAATCCAATAACAG
Found at i:13734 original size:61 final size:60
Alignment explanation
Indices: 13681--13794 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
13671 TAAAGACTCG
* * *
13681 ATCTTTTACTTTTGGCCAAATAAAGG-CCTAATGTT-ATCGAAAATGCTCAAATAAAGGTCCA
1 ATCTTTTA-ATTTGGCCAAAT-AAGGACCTAAAGTTAAT-GAAAATGCTCAAATAAAGCTCCA
* *
13742 ATCTTTTAATTTGGTCAAATAAGGATCTAAAGTTAATGAAAATGCTCAAATAA
1 ATCTTTTAATTTGGCCAAATAAGGACCTAAAGTTAATGAAAATGCTCAAATAA
13795 GAGTCTGTCT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
59 4 0.09
60 33 0.70
61 10 0.21
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (60 bp):
ATCTTTTAATTTGGCCAAATAAGGACCTAAAGTTAATGAAAATGCTCAAATAAAGCTCCA
Found at i:13935 original size:29 final size:29
Alignment explanation
Indices: 13875--13940 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 29
13865 ACGTGAGGTT
* *
13875 CTTATTTGGCTAAATTAAAAGATCGGATC
1 CTTATTTGGCTAAATTAAAAGATCAGACC
* *
13904 CTTATTTTGCTAAATTAAAAGATCAGCCC
1 CTTATTTGGCTAAATTAAAAGATCAGACC
13933 CTTATTTG
1 CTTATTTG
13941 AGCATTTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.38
Consensus pattern (29 bp):
CTTATTTGGCTAAATTAAAAGATCAGACC
Found at i:17309 original size:2 final size:2
Alignment explanation
Indices: 17304--17368 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
17294 AATCCAAACG
17304 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
17346 GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA G
17369 TAGT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Done.