Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013677.1 Corchorus olitorius cultivar O-4 contig13710, 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: 48132
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--54 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C- CT C- CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
41 CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT
55 TTCTATTTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 48 0.96
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:746 original size:64 final size:64
Alignment explanation
Indices: 663--786 Score: 194
Period size: 64 Copynumber: 1.9 Consensus size: 64
653 TAATTGACTG
663 AATTTAACTGTACCAACCTATTGAATTATGAAGGGTCCAACGTAGGACAATAATTTACGGGCTC
1 AATTTAACTGTACCAACCTATTGAATTATGAAGGGTCCAACGTAGGACAATAATTTACGGGCTC
* ** * * *
727 AATTTAATTGTACCAACCTATTGTTTTATGAAGGGTCCCAGGTTGGACAATAATTTACGG
1 AATTTAACTGTACCAACCTATTGAATTATGAAGGGTCCAACGTAGGACAATAATTTACGG
787 ATATGATGAA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Consensus pattern (64 bp):
AATTTAACTGTACCAACCTATTGAATTATGAAGGGTCCAACGTAGGACAATAATTTACGGGCTC
Found at i:2695 original size:15 final size:15
Alignment explanation
Indices: 2675--2708 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
2665 AGGAAAAAGT
*
2675 GCAAAGAAATAATGG
1 GCAAAGAAAGAATGG
2690 GCAAAGAAAGAATGG
1 GCAAAGAAAGAATGG
2705 GCAA
1 GCAA
2709 TGAATTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.53, C:0.09, G:0.29, T:0.09
Consensus pattern (15 bp):
GCAAAGAAAGAATGG
Found at i:3182 original size:42 final size:42
Alignment explanation
Indices: 3126--3243 Score: 164
Period size: 42 Copynumber: 2.8 Consensus size: 42
3116 ATTTTTGTTA
3126 TTTAATTAAGGTGAAAGTAAATATAGAATGAATTAAAAGTTG
1 TTTAATTAAGGTGAAAGTAAATATAGAATGAATTAAAAGTTG
* * * *
3168 TTTAATTAATGTGAAAGTAAACATAGAATGCATTAAATGTTG
1 TTTAATTAAGGTGAAAGTAAATATAGAATGAATTAAAAGTTG
* * * *
3210 TTTAATTAAGGTAAAAATAAATATAAAACGAATT
1 TTTAATTAAGGTGAAAGTAAATATAGAATGAATT
3244 GAAGTTGATT
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.48, C:0.03, G:0.15, T:0.34
Consensus pattern (42 bp):
TTTAATTAAGGTGAAAGTAAATATAGAATGAATTAAAAGTTG
Found at i:4280 original size:64 final size:64
Alignment explanation
Indices: 4179--4300 Score: 226
Period size: 64 Copynumber: 1.9 Consensus size: 64
4169 ATAATTGATT
*
4179 CAATTTAATTGTACCAACATATTGTTTTATGAAGGGTCCAACGTAGGACAATAATTTAAGGACG
1 CAATTTAATTGTACCAACATATTGTTATATGAAGGGTCCAACGTAGGACAATAATTTAAGGACG
*
4243 CAATTTAATTGTACCAACCTATTGTTATATGAAGGGTCCAACGTAGGACAATAATTTA
1 CAATTTAATTGTACCAACATATTGTTATATGAAGGGTCCAACGTAGGACAATAATTTA
4301 CGGATATGAT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 56 1.00
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (64 bp):
CAATTTAATTGTACCAACATATTGTTATATGAAGGGTCCAACGTAGGACAATAATTTAAGGACG
Found at i:4373 original size:12 final size:12
Alignment explanation
Indices: 4347--4406 Score: 93
Period size: 12 Copynumber: 4.9 Consensus size: 12
4337 AGATATCCAT
4347 GGATATATCGAAC
1 GGATATATCG-AC
4360 GGATATATCGAC
1 GGATATATCGAC
*
4372 GGATATATCGAT
1 GGATATATCGAC
*
4384 GGATATATCGGC
1 GGATATATCGAC
4396 GGATATATCGA
1 GGATATATCGA
4407 GGTATCGATG
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
12 33 0.77
13 10 0.23
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (12 bp):
GGATATATCGAC
Found at i:5502 original size:10 final size:10
Alignment explanation
Indices: 5487--5542 Score: 103
Period size: 10 Copynumber: 5.6 Consensus size: 10
5477 AATTTAATAT
5487 GGATATTTAC
1 GGATATTTAC
5497 GGATATTTAC
1 GGATATTTAC
5507 GGATATTTAC
1 GGATATTTAC
*
5517 AGATATTTAC
1 GGATATTTAC
5527 GGATATTTAC
1 GGATATTTAC
5537 GGATAT
1 GGATAT
5543 ATCGAGGTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 44 1.00
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (10 bp):
GGATATTTAC
Found at i:5660 original size:20 final size:20
Alignment explanation
Indices: 5617--5661 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
5607 CCAGGGGTAC
5617 ATATATCGGATATATCGACAA
1 ATATATCGGATATA-CGACAA
*
5638 ATATATCGAGATATA-GACGA
1 ATATATCG-GATATACGACAA
5658 ATAT
1 ATAT
5662 TTAATTCAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 8 0.36
21 8 0.36
22 6 0.27
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.29
Consensus pattern (20 bp):
ATATATCGGATATACGACAA
Found at i:9566 original size:26 final size:26
Alignment explanation
Indices: 9535--9585 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
9525 TCTAAGTATA
9535 TTAATTTATCTCCTTTATTCTTTATG
1 TTAATTTATCTCCTTTATTCTTTATG
9561 TTAATTTATCTCCTTTATTCTTTAT
1 TTAATTTATCTCCTTTATTCTTTAT
9586 TTTCACTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.20, C:0.16, G:0.02, T:0.63
Consensus pattern (26 bp):
TTAATTTATCTCCTTTATTCTTTATG
Found at i:14970 original size:14 final size:14
Alignment explanation
Indices: 14951--14985 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
14941 GGCAATTAAT
14951 AAAGAAAACAATAA
1 AAAGAAAACAATAA
*
14965 AAAGAAAGCAATAA
1 AAAGAAAACAATAA
*
14979 TAAGAAA
1 AAAGAAA
14986 TCATACTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.74, C:0.06, G:0.11, T:0.09
Consensus pattern (14 bp):
AAAGAAAACAATAA
Found at i:15577 original size:19 final size:18
Alignment explanation
Indices: 15553--15588 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
15543 TAAAGATTTA
15553 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
15572 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
15589 ATTATCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:19040 original size:28 final size:29
Alignment explanation
Indices: 18997--19072 Score: 95
Period size: 28 Copynumber: 2.7 Consensus size: 29
18987 ACAAGGTTAA
**
18997 AAGGGTAAAATTGTAAATTTAAC-C-TTCT
1 AAGGGTAAAACGGT-AATTTAACTCATTCT
19025 AAGGGTAAAACGGTAATTT-ACTCATTCT
1 AAGGGTAAAACGGTAATTTAACTCATTCT
*
19053 TAGGGTAAAACGGTAATTTA
1 AAGGGTAAAACGGTAATTTA
19073 TGCCTATACA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
26 2 0.05
27 6 0.14
28 34 0.81
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (29 bp):
AAGGGTAAAACGGTAATTTAACTCATTCT
Found at i:20024 original size:23 final size:24
Alignment explanation
Indices: 19988--20033 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
19978 CTGGGCCATA
19988 GCTGGCTCGTGCGCCAGGCCTGGGC
1 GCTGGCTCG-GCGCCAGGCCTGGGC
*
20013 GCTGGCTC-GCGCCTGGCCTGG
1 GCTGGCTCGGCGCCAGGCCTGG
20034 CCCAAGTGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 12 0.60
25 8 0.40
ACGTcount: A:0.02, C:0.37, G:0.43, T:0.17
Consensus pattern (24 bp):
GCTGGCTCGGCGCCAGGCCTGGGC
Found at i:24700 original size:18 final size:19
Alignment explanation
Indices: 24677--24712 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
24667 CTCCTCTATC
*
24677 ATGAAAA-ACTTTTTTTTT
1 ATGAAAACAATTTTTTTTT
24695 ATGAAAACAATTTTTTTT
1 ATGAAAACAATTTTTTTT
24713 AATTACCCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.53
Consensus pattern (19 bp):
ATGAAAACAATTTTTTTTT
Found at i:32467 original size:11 final size:11
Alignment explanation
Indices: 32451--32476 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
32441 GTTTTAGATC
32451 TTTTCTTCTAG
1 TTTTCTTCTAG
32462 TTTTCTTCTAG
1 TTTTCTTCTAG
32473 TTTT
1 TTTT
32477 TTAGGCAAGG
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:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:33608 original size:23 final size:21
Alignment explanation
Indices: 33578--33626 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 21
33568 CGGTTTTCTA
33578 TTTTGCGTCGA-AAAAAAATATAT
1 TTTTGCGTC-ATAAAAAAAT-T-T
33601 TTTTGCGTCATAAAAAAATTT
1 TTTTGCGTCATAAAAAAATTT
33622 TTTTG
1 TTTTG
33627 TTTCTGCGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.24
22 2 0.08
23 17 0.68
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.43
Consensus pattern (21 bp):
TTTTGCGTCATAAAAAAATTT
Found at i:33652 original size:23 final size:24
Alignment explanation
Indices: 33626--33672 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
33616 AAATTTTTTT
33626 GTTTCTGCG-TCTTATAAAAAAAA
1 GTTTCTGCGTTCTTATAAAAAAAA
* * *
33649 GTTTTTGCGTTTTTCTAAAAAAAA
1 GTTTCTGCGTTCTTATAAAAAAAA
33673 AGAGTTTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (24 bp):
GTTTCTGCGTTCTTATAAAAAAAA
Found at i:39156 original size:11 final size:11
Alignment explanation
Indices: 39140--39165 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
39130 GTTTTAGATC
39140 TTTTCTTCTAG
1 TTTTCTTCTAG
39151 TTTTCTTCTAG
1 TTTTCTTCTAG
39162 TTTT
1 TTTT
39166 TTAGGCAAGG
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:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:39933 original size:15 final size:16
Alignment explanation
Indices: 39900--39941 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
39890 TTACTCTGCT
39900 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
39916 TTGTTTTCT-GCT-TAA
1 TTGTTTTCTAG-TATAA
39931 TTGTTATTCTA
1 TTGTT-TTCTA
39942 AACCCTCTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.19, C:0.10, G:0.12, T:0.60
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:40954 original size:19 final size:18
Alignment explanation
Indices: 40921--40956 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
40911 TTGAAATTAT
40921 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
40939 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
40957 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:43216 original size:32 final size:35
Alignment explanation
Indices: 43180--43249 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
43170 TTTTCAAAAT
*
43180 AACTAAACT-AA-A-CTAGAAAACAATTTTAATAA
1 AACTAAACTAAAGATCTAGAAAACAATTTTAACAA
*
43212 AACTAAACTAAAGATCTAGAAAATAATTTTAACAA
1 AACTAAACTAAAGATCTAGAAAACAATTTTAACAA
43247 AAC
1 AAC
43250 AATTAATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
32 9 0.27
33 2 0.06
34 1 0.03
35 21 0.64
ACGTcount: A:0.59, C:0.13, G:0.04, T:0.24
Consensus pattern (35 bp):
AACTAAACTAAAGATCTAGAAAACAATTTTAACAA
Found at i:45918 original size:17 final size:17
Alignment explanation
Indices: 45893--45936 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
45883 CCGAACCCGC
*
45893 CCGAACCCGA-CCCGAGA
1 CCGAGCCCGATCCCGA-A
*
45910 CCGAGCCCGATCCCGAC
1 CCGAGCCCGATCCCGAA
45927 CCGAGCCCGA
1 CCGAGCCCGA
45937 ACTCGAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 19 0.79
18 5 0.21
ACGTcount: A:0.23, C:0.50, G:0.25, T:0.02
Consensus pattern (17 bp):
CCGAGCCCGATCCCGAA
Found at i:45918 original size:23 final size:23
Alignment explanation
Indices: 45891--45936 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
45881 TCCCGAACCC
45891 GCCCGAACCCGACCCGAGACCGA
1 GCCCGAACCCGACCCGAGACCGA
* *
45914 GCCCGATCCCGACCCGAGCCCGA
1 GCCCGAACCCGACCCGAGACCGA
45937 ACTCGAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.50, G:0.26, T:0.02
Consensus pattern (23 bp):
GCCCGAACCCGACCCGAGACCGA
Found at i:46744 original size:13 final size:12
Alignment explanation
Indices: 46708--46754 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
46698 TCAATCTTTA
*
46708 TATATATTGATAA
1 TATATATT-ATAT
*
46721 TA-ATGTTATAT
1 TATATATTATAT
46732 TATATTATTATAT
1 TATA-TATTATAT
46745 TATATATTAT
1 TATATATTAT
46755 CAATAAACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:46925 original size:16 final size:16
Alignment explanation
Indices: 46904--47024 Score: 122
Period size: 16 Copynumber: 7.6 Consensus size: 16
46894 CCGACCCGAG
46904 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
*
46920 CCCGAACCCG-ACATAA
1 CCCGAACCCGAAAAT-A
*
46936 CCCGAGCCCGAAAATA
1 CCCGAACCCGAAAATA
**
46952 CCCGAACCCG-ACTTAA
1 CCCGAACCCGAAAAT-A
* *
46968 CCCGAGCCCAAAAATA
1 CCCGAACCCGAAAATA
*
46984 CCCGAACCCGAAAAAA
1 CCCGAACCCGAAAATA
* *
47000 CCTGAACCC-AAAGTA
1 CCCGAACCCGAAAATA
47015 CCCGAACCCG
1 CCCGAACCCG
47025 CCCAATTGCC
Statistics
Matches: 83, Mismatches: 17, Indels: 10
0.75 0.15 0.09
Matches are distributed among these distances:
15 17 0.20
16 61 0.73
17 5 0.06
ACGTcount: A:0.39, C:0.40, G:0.14, T:0.07
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:46946 original size:32 final size:32
Alignment explanation
Indices: 46904--47024 Score: 163
Period size: 32 Copynumber: 3.8 Consensus size: 32
46894 CCGACCCGAG
46904 CCCGAACCCGAAAATACCCGAACCCGACATAA
1 CCCGAACCCGAAAATACCCGAACCCGACATAA
* *
46936 CCCGAGCCCGAAAATACCCGAACCCGACTTAA
1 CCCGAACCCGAAAATACCCGAACCCGACATAA
* * * *
46968 CCCGAGCCCAAAAATACCCGAACCCGAAAAAA
1 CCCGAACCCGAAAATACCCGAACCCGACATAA
* *
47000 CCTGAACCC-AAAGTACCCGAACCCG
1 CCCGAACCCGAAAATACCCGAACCCG
47025 CCCAATTGCC
Statistics
Matches: 80, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
31 15 0.19
32 65 0.81
ACGTcount: A:0.39, C:0.40, G:0.14, T:0.07
Consensus pattern (32 bp):
CCCGAACCCGAAAATACCCGAACCCGACATAA
Found at i:47651 original size:27 final size:26
Alignment explanation
Indices: 47621--47691 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 26
47611 GTACAGCCAT
47621 CGGTAAGTTCATCT-CAAGTTTTTCCTA
1 CGGTAA-TTCATCTCCAA-TTTTTCCTA
* *
47648 CGGTGAATTCATCTCCAATTTTTCTTG
1 CGGT-AATTCATCTCCAATTTTTCCTA
*
47675 CGGTAATTGATTCTCCA
1 CGGTAATTCA-TCTCCA
47692 GATCTTCCTG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
26 5 0.13
27 28 0.74
28 5 0.13
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (26 bp):
CGGTAATTCATCTCCAATTTTTCCTA
Done.