Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023765.1 Corchorus olitorius cultivar O-4 contig23798, 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: 24449
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:591 original size:14 final size:14
Alignment explanation
Indices: 551--597 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
541 AAGTATTTAC
*
551 TTTTAAAAATTATTT
1 TTTTTAAAA-TATTT
*
566 TGTTTT-ATATATTT
1 T-TTTTAAAATATTT
580 TTTTTAAAATATTT
1 TTTTTAAAATATTT
594 TTTT
1 TTTT
598 ATAGAAACCG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
13 4 0.15
14 17 0.63
15 3 0.11
16 3 0.11
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (14 bp):
TTTTTAAAATATTT
Found at i:14556 original size:30 final size:30
Alignment explanation
Indices: 14473--14558 Score: 136
Period size: 30 Copynumber: 2.9 Consensus size: 30
14463 CAGCTTTATC
* *
14473 TTCTACAATTCGCTCCTTACAATAATTCTT
1 TTCTGCAATTCGCTCCTTACAATCATTCTT
*
14503 TTCTGCAATTTGCTCCTTACAATCATTCTT
1 TTCTGCAATTCGCTCCTTACAATCATTCTT
*
14533 TTCTGCAATTCGGTCCTTACAATCAT
1 TTCTGCAATTCGCTCCTTACAATCAT
14559 AGAAATATAG
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.23, C:0.27, G:0.07, T:0.43
Consensus pattern (30 bp):
TTCTGCAATTCGCTCCTTACAATCATTCTT
Found at i:17363 original size:33 final size:33
Alignment explanation
Indices: 17326--17391 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
17316 GGAGGCACTG
* *
17326 ACCATGGAATTCCGCCCTAGGAGGGCGGCACCA
1 ACCATGGAATGCCGCCCAAGGAGGGCGGCACCA
* *
17359 ACCATGGCATGCCGCCCAAGGAGGGTGGCACCA
1 ACCATGGAATGCCGCCCAAGGAGGGCGGCACCA
17392 GTTATTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.33, G:0.32, T:0.11
Consensus pattern (33 bp):
ACCATGGAATGCCGCCCAAGGAGGGCGGCACCA
Found at i:18548 original size:30 final size:31
Alignment explanation
Indices: 18485--18561 Score: 102
Period size: 30 Copynumber: 2.5 Consensus size: 31
18475 AAAAAATGAG
*
18485 TCAGGGACCCAATTGCTCAATTAACTCCACT
1 TCAGGGACCCAATTGCTCAACTAACTCCACT
* * *
18516 TCAGGGACTCAATTGCTC-ACTAAGTTCACT
1 TCAGGGACCCAATTGCTCAACTAACTCCACT
*
18546 TCAGGGACCCATTTGC
1 TCAGGGACCCAATTGC
18562 ACATTTACCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 23 0.57
31 17 0.43
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (31 bp):
TCAGGGACCCAATTGCTCAACTAACTCCACT
Found at i:20945 original size:77 final size:79
Alignment explanation
Indices: 20827--20980 Score: 249
Period size: 77 Copynumber: 2.0 Consensus size: 79
20817 GTTAAAAATT
*
20827 TAAAATAGTAAAATAATAAAACTAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATAATAAAACTAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAG
20892 AG-TTTTAGTTGTG
66 AGTTTTTAGTTGTG
** * *
20905 TAAAATAGTAAAATGGTAAAA-TAAAATAGTTATAAAGATATTAGATTTAATTAAATAAATATGG
1 TAAAATAGTAAAATAATAAAACTAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAG
20969 AGTTTTTAGTTG
66 AGTTTTTAGTTG
20981 AGTACAACTA
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
77 42 0.60
78 28 0.40
ACGTcount: A:0.50, C:0.01, G:0.14, T:0.36
Consensus pattern (79 bp):
TAAAATAGTAAAATAATAAAACTAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAG
AGTTTTTAGTTGTG
Found at i:21582 original size:18 final size:18
Alignment explanation
Indices: 21559--21593 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
21549 ACAAAAATTG
21559 AAATTGTTCATAAACAAA
1 AAATTGTTCATAAACAAA
*
21577 AAATTGTTCATGAACAA
1 AAATTGTTCATAAACAA
21594 TGTAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (18 bp):
AAATTGTTCATAAACAAA
Found at i:21660 original size:15 final size:14
Alignment explanation
Indices: 21632--21673 Score: 61
Period size: 15 Copynumber: 3.1 Consensus size: 14
21622 AACGAACAAA
21632 ATAT-TATATAATT
1 ATATATATATAATT
21645 ATATATATATATATT
1 ATATATATATA-ATT
21660 ATATATA-ATAATT
1 ATATATATATAATT
21673 A
1 A
21674 AATTTTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 8 0.30
14 9 0.33
15 10 0.37
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATATATATATAATT
Found at i:21746 original size:16 final size:16
Alignment explanation
Indices: 21725--21756 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
21715 TTTATAATTT
21725 TTATTAATAATATATA
1 TTATTAATAATATATA
*
21741 TTATTATTAATATATA
1 TTATTAATAATATATA
21757 AATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATTAATAATATATA
Found at i:21749 original size:19 final size:19
Alignment explanation
Indices: 21725--21772 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
21715 TTTATAATTT
* *
21725 TTATTAATAATATATATTA
1 TTATTAATAATATAAATAA
21744 TTATTAAT-ATATAAATAA
1 TTATTAATAATATAAATAA
21762 TTATATAATAA
1 TTAT-TAATAA
21773 ACGAACGTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 12 0.48
19 12 0.48
20 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTATTAATAATATAAATAA
Found at i:21844 original size:35 final size:35
Alignment explanation
Indices: 21798--21905 Score: 207
Period size: 35 Copynumber: 3.1 Consensus size: 35
21788 TTATATAAAC
*
21798 GAACACTTAAATGAACAATAAACGAGCCTATTCGT
1 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
21833 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
1 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
21868 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
1 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
21903 GAA
1 GAA
21906 TATAAAAGAA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
35 72 1.00
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (35 bp):
GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
Found at i:22546 original size:9 final size:9
Alignment explanation
Indices: 22516--22551 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
22506 CCCAAATTAC
22516 TTATGGAAA
1 TTATGGAAA
*
22525 TTAAGGAAA
1 TTATGGAAA
22534 TTATGGAAA
1 TTATGGAAA
22543 TTAT-GAAA
1 TTATGGAAA
22551 T
1 T
22552 CAAATGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 5 0.20
9 20 0.80
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.33
Consensus pattern (9 bp):
TTATGGAAA
Found at i:23957 original size:49 final size:47
Alignment explanation
Indices: 23828--23969 Score: 178
Period size: 49 Copynumber: 3.0 Consensus size: 47
23818 CAAGCAATCC
* * * *
23828 TTTACTTTTCACTGCACTTTTTCTCAATTTTTACCACAAAATTGAACT
1 TTTAATTTTCATTGCACTTTTTCTCAATTTTTA-GACAAAATTGATCT
*
23876 TTT-ATTTTTACTTGCATCTTTTTCTCAATTTTTAAGACAAAATTGATCT
1 TTTAATTTTCA-TTGCA-CTTTTTCTCAATTTTT-AGACAAAATTGATCT
* *
23925 TTTAATTTTCATTGCACTTTTTATCAATTTTTTGACAAAATTGAT
1 TTTAATTTTCATTGCACTTTTTCTCAATTTTTAGACAAAATTGAT
23970 TGGCACGCTC
Statistics
Matches: 82, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
47 17 0.21
48 22 0.27
49 36 0.44
50 7 0.09
ACGTcount: A:0.27, C:0.16, G:0.06, T:0.51
Consensus pattern (47 bp):
TTTAATTTTCATTGCACTTTTTCTCAATTTTTAGACAAAATTGATCT
Done.