Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020048.1 Corchorus olitorius cultivar O-4 contig20081, 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: 87323
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:6487 original size:33 final size:33
Alignment explanation
Indices: 6434--6535 Score: 134
Period size: 33 Copynumber: 3.1 Consensus size: 33
6424 GCTCTTACAA
*
6434 ACAATGAAG-TTACGGGCCTTCATCACGCCGTT
1 ACAATGAAGCTCACGGGCCTTCATCACGCCGTT
* * *
6466 CCAATGAAGCTCATGGGCCTTCATCACGCCTTT
1 ACAATGAAGCTCACGGGCCTTCATCACGCCGTT
* * *
6499 ACAATGAAGTTCACGGGCCTTCATCACACCTTT
1 ACAATGAAGCTCACGGGCCTTCATCACGCCGTT
6532 ACAA
1 ACAA
6536 GTTGAGCAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
32 8 0.13
33 53 0.87
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.25
Consensus pattern (33 bp):
ACAATGAAGCTCACGGGCCTTCATCACGCCGTT
Found at i:25378 original size:16 final size:16
Alignment explanation
Indices: 25357--25433 Score: 52
Period size: 16 Copynumber: 4.9 Consensus size: 16
25347 GGTTAACTTC
*
25357 TCGGGTTATTCGGGTT
1 TCGGGTCATTCGGGTT
*
25373 TCGGGTCATTTGGGTT
1 TCGGGTCATTCGGGTT
* * *
25389 ACAGGTCATT-AGGTCT
1 TCGGGTCATTCGGGT-T
*
25405 T-GGGTCA-TCTGGTT
1 TCGGGTCATTCGGGTT
* *
25419 GCAGGTCATTCGGGT
1 TCGGGTCATTCGGGT
25434 CGGGTGGGTT
Statistics
Matches: 46, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
14 2 0.04
15 16 0.35
16 28 0.61
ACGTcount: A:0.12, C:0.16, G:0.35, T:0.38
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:27622 original size:1 final size:1
Alignment explanation
Indices: 27616--27649 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
27606 GATTAAACTT
27616 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
27650 CCCGACAACG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:28763 original size:14 final size:13
Alignment explanation
Indices: 28730--28812 Score: 62
Period size: 12 Copynumber: 7.2 Consensus size: 13
28720 AACCGTTTAA
28730 TAATTATATATAT
1 TAATTATATATAT
*
28743 T-ATTATATAT-G
1 TAATTATATATAT
28754 TAATTATATATAT
1 TAATTATATATAT
28767 CTAA-TAT-TAT-T
1 -TAATTATATATAT
28778 T--TT-TATATA-
1 TAATTATATATAT
28787 TAA-TATATAT-T
1 TAATTATATATAT
*
28798 TAATTATAAATAT
1 TAATTATATATAT
28811 TA
1 TA
28813 CTAAACGATC
Statistics
Matches: 55, Mismatches: 3, Indels: 24
0.67 0.04 0.29
Matches are distributed among these distances:
8 1 0.02
9 5 0.09
10 2 0.04
11 10 0.18
12 27 0.49
13 7 0.13
14 3 0.05
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (13 bp):
TAATTATATATAT
Found at i:35761 original size:53 final size:53
Alignment explanation
Indices: 35702--35806 Score: 174
Period size: 53 Copynumber: 2.0 Consensus size: 53
35692 AACCAAGCAA
**
35702 ATCCTAAATATTTGAATCTTAATAAAAAGATCGAGTTTTCACCAACAAAATAT
1 ATCCTAAATATTTGAATCTTAATAAAAAGATCGAACTTTCACCAACAAAATAT
* *
35755 ATCCTAAATATTTGAATCTTAATAAAAAGATTGAACTTTCACTAACAAAATA
1 ATCCTAAATATTTGAATCTTAATAAAAAGATCGAACTTTCACCAACAAAATA
35807 CTCCTTCCGT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.47, C:0.14, G:0.07, T:0.32
Consensus pattern (53 bp):
ATCCTAAATATTTGAATCTTAATAAAAAGATCGAACTTTCACCAACAAAATAT
Found at i:39533 original size:33 final size:34
Alignment explanation
Indices: 39495--39558 Score: 112
Period size: 33 Copynumber: 1.9 Consensus size: 34
39485 ATCAAGAAAA
*
39495 TAAACTGAGATAAACTTATG-AAAATATTTTCTC
1 TAAACTAAGATAAACTTATGAAAAATATTTTCTC
39528 TAAACTAAGATAAACTTATGAAAAATATTTT
1 TAAACTAAGATAAACTTATGAAAAATATTTT
39559 TTTTCTACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 19 0.66
34 10 0.34
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.36
Consensus pattern (34 bp):
TAAACTAAGATAAACTTATGAAAAATATTTTCTC
Found at i:40843 original size:30 final size:31
Alignment explanation
Indices: 40800--40874 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
40790 TTTAGCCACT
* **
40800 AATTTGAGTCTAAACCTTTC-AAAGTTGCTC
1 AATTTGAGCCTAAACCTTTCAAAAGTTGAAC
*
40830 AATTTGGGCCTAAACCTTTCAAAAGTTGAAC
1 AATTTGAGCCTAAACCTTTCAAAAGTTGAAC
40861 AATTTGAGCCTAAA
1 AATTTGAGCCTAAA
40875 AACAGAAACG
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 18 0.46
31 21 0.54
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.32
Consensus pattern (31 bp):
AATTTGAGCCTAAACCTTTCAAAAGTTGAAC
Found at i:43566 original size:10 final size:10
Alignment explanation
Indices: 43551--43597 Score: 58
Period size: 10 Copynumber: 4.6 Consensus size: 10
43541 AATTTAATGC
*
43551 TTAATTTGTT
1 TTAATTTGTA
43561 TTAATTTGTA
1 TTAATTTGTA
*
43571 ATAATTTAGTA
1 TTAATTT-GTA
*
43582 TTAATTAGTA
1 TTAATTTGTA
43592 TTAATT
1 TTAATT
43598 AATTTAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
10 24 0.75
11 8 0.25
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (10 bp):
TTAATTTGTA
Found at i:43568 original size:31 final size:31
Alignment explanation
Indices: 43497--43578 Score: 76
Period size: 31 Copynumber: 2.6 Consensus size: 31
43487 GTTTATCAAC
* *
43497 TTTTAATTTGTTTAATTTAAGGTTTTCATTT
1 TTTTAATTTGTTTAATTTAAGGTCTTAATTT
** * *
43528 TAATGATTTGTTTAATTTAATG-CTTAATTT
1 TTTTAATTTGTTTAATTTAAGGTCTTAATTT
*
43558 GTTTTAATTTGTAATAATTTA
1 -TTTTAATTTGT-TTAATTTA
43579 GTATTAATTA
Statistics
Matches: 39, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
30 6 0.15
31 26 0.67
32 7 0.18
ACGTcount: A:0.28, C:0.02, G:0.10, T:0.60
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGGTCTTAATTT
Found at i:43587 original size:21 final size:20
Alignment explanation
Indices: 43552--43597 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
43542 ATTTAATGCT
* *
43552 TAATTTGTTTTAATTTGTAA
1 TAATTTGTATTAATTAGTAA
*
43572 TAATTTAGTATTAATTAGTAT
1 TAATTT-GTATTAATTAGTAA
43593 TAATT
1 TAATT
43598 AATTTAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.57
Consensus pattern (20 bp):
TAATTTGTATTAATTAGTAA
Found at i:43598 original size:10 final size:10
Alignment explanation
Indices: 43551--43607 Score: 53
Period size: 10 Copynumber: 5.7 Consensus size: 10
43541 AATTTAATGC
* *
43551 TTAATTTGTT
1 TTAATTAGTA
*
43561 TTAATTTGTA
1 TTAATTAGTA
*
43571 ATAATTTAGTA
1 TTAA-TTAGTA
43582 TTAATTAGTA
1 TTAATTAGTA
*
43592 TTAATTAAT-
1 TTAATTAGTA
43601 TTAATTA
1 TTAATTA
43608 TTGTTAAACT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
9 7 0.17
10 26 0.63
11 8 0.20
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (10 bp):
TTAATTAGTA
Found at i:43863 original size:17 final size:17
Alignment explanation
Indices: 43835--43882 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
43825 TTAATCTTTA
43835 TATATATATATTGA-TAAT
1 TATAT-TATATT-ATTAAT
*
43853 TATGTTATATTATTAAT
1 TATATTATATTATTAAT
43870 TATATTATATTAT
1 TATATTATATTAT
43883 CAATAAACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 1 0.04
17 22 0.81
18 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (17 bp):
TATATTATATTATTAAT
Found at i:47332 original size:31 final size:31
Alignment explanation
Indices: 47297--47359 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
47287 CTCGAGCTCA
* * *
47297 AATAGCCAATTATTCGACTCGACTCAATCCG
1 AATAGCCAACTATTCGACACGACTCAACCCG
47328 AATAGCCAACTATTCGACACGACTCAACCCG
1 AATAGCCAACTATTCGACACGACTCAACCCG
47359 A
1 A
47360 TTACACTCCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.35, C:0.32, G:0.13, T:0.21
Consensus pattern (31 bp):
AATAGCCAACTATTCGACACGACTCAACCCG
Found at i:58685 original size:38 final size:38
Alignment explanation
Indices: 58643--58725 Score: 112
Period size: 38 Copynumber: 2.2 Consensus size: 38
58633 CTCGAGCTGA
* *
58643 GCTCGATTCGATACACGATTTATCTGAACTCGAACTCG
1 GCTCGATTCGATACACAAATTATCTGAACTCGAACTCG
** **
58681 GCTCGATTCGATACTTAAATTATCTGAACTCGAGTTCG
1 GCTCGATTCGATACACAAATTATCTGAACTCGAACTCG
58719 GCTCGAT
1 GCTCGAT
58726 AACGACCGAG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.31
Consensus pattern (38 bp):
GCTCGATTCGATACACAAATTATCTGAACTCGAACTCG
Found at i:61533 original size:32 final size:32
Alignment explanation
Indices: 61491--61552 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
61481 ATTTTGAATC
61491 TTATAAATGAAAAAAATAAACACCAAAATCTT
1 TTATAAATGAAAAAAATAAACACCAAAATCTT
*
61523 TTATCAATGAAAAAAATAAACACCAAAATC
1 TTATAAATGAAAAAAATAAACACCAAAATC
61553 CATTGTTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.60, C:0.15, G:0.03, T:0.23
Consensus pattern (32 bp):
TTATAAATGAAAAAAATAAACACCAAAATCTT
Found at i:72949 original size:31 final size:32
Alignment explanation
Indices: 72903--72962 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
72893 ATTTCATACA
*
72903 AGTCTCGAGGGTAATTTGGGCA-TCCAATATT
1 AGTCTCGAGGATAATTTGGGCATTCCAATATT
*
72934 AGTCTTGAGGATAATTTGGGCATTCCAAT
1 AGTCTCGAGGATAATTTGGGCATTCCAAT
72963 TCTTTTTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 20 0.77
32 6 0.23
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (32 bp):
AGTCTCGAGGATAATTTGGGCATTCCAATATT
Found at i:72993 original size:13 final size:13
Alignment explanation
Indices: 72975--72999 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
72965 TTTTTTACCC
72975 TTCACTTTGGATA
1 TTCACTTTGGATA
72988 TTCACTTTGGAT
1 TTCACTTTGGAT
73000 TTTGGCTTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (13 bp):
TTCACTTTGGATA
Found at i:73128 original size:31 final size:32
Alignment explanation
Indices: 73076--73138 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 32
73066 GGGTTTAGGT
73076 TTCATGTCATGTCATTTTTTGTCTCCTTGAGAC
1 TTCATGTCATGTCATTTTTTGTCTCCTT-AGAC
*
73109 TTCATGTCAT-T-TTTTTTTGTCTCCTTAGAC
1 TTCATGTCATGTCATTTTTTGTCTCCTTAGAC
73139 CATTATTTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 4 0.14
31 14 0.48
32 1 0.03
33 10 0.34
ACGTcount: A:0.14, C:0.21, G:0.13, T:0.52
Consensus pattern (32 bp):
TTCATGTCATGTCATTTTTTGTCTCCTTAGAC
Found at i:73241 original size:11 final size:11
Alignment explanation
Indices: 73215--73244 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
73205 TTAATATTTA
73215 ATTTTAGTTTG
1 ATTTTAGTTTG
73226 A-TTTAGTTTG
1 ATTTTAGTTTG
73236 ATTTTAGTT
1 ATTTTAGTT
73245 ATTTGATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.20, C:0.00, G:0.17, T:0.63
Consensus pattern (11 bp):
ATTTTAGTTTG
Found at i:74936 original size:15 final size:14
Alignment explanation
Indices: 74914--74943 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
74904 GTTTTGTTTC
74914 ATTTAATTTTAATA
1 ATTTAATTTTAATA
74928 ATTTCAATTTTAATA
1 ATTT-AATTTTAATA
74943 A
1 A
74944 AATTATTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTTAATTTTAATA
Found at i:77531 original size:16 final size:16
Alignment explanation
Indices: 77510--77542 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
77500 TTATAATTCA
77510 TCCATTTAACTTTTCG
1 TCCATTTAACTTTTCG
77526 TCCATTTAACTTTTCG
1 TCCATTTAACTTTTCG
77542 T
1 T
77543 GGTTGGATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.24, G:0.06, T:0.52
Consensus pattern (16 bp):
TCCATTTAACTTTTCG
Done.