Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012711.1 Corchorus olitorius cultivar O-4 contig12744, 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: 58165
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:116 original size:68 final size:68
Alignment explanation
Indices: 9--608 Score: 914
Period size: 68 Copynumber: 9.0 Consensus size: 68
1 GAAAAAGA
* * *
9 AAAATACTAAACTTAAATGC-AAAAGATGAAAATGACCCTTCGAACGAAAGGGTATTTTTGGAAA
1 AAAACACTAAACTTAAATGCAAAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAA
73 TAG
66 TAG
* *
76 AAAACACTAAACTTAAATACAAAAGGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAA
1 AAAACACTAAACTTAAATGCAAAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAA
141 TAG
66 TAG
* * *
144 AAAACACTAAACTTAAATGCAAAAGGACGAAAATGACCCTTCGATCGAAAGGGTATTTCTGGAAA
1 AAAACACTAAACTTAAATGCAAAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAA
209 TAG
66 TAG
*
212 AAAACACTAAACTTAAATGGAAAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAA
1 AAAACACTAAACTTAAATGCAAAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAA
*
277 TAT
66 TAG
*
280 AAAACACTAAACTTAAATGCAAAAGGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAA
1 AAAACACTAAACTTAAATGCAAAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAA
345 TAG
66 TAG
* * * *
348 AAAACACTAAACTTAAATGCAAAAGGATGAAAATGACCCTTCGACCGAAATGGTAATTTTGGAAA
1 AAAACACTAAACTTAAATGCAAAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAA
413 TAG
66 TAG
* ** *
416 AAAACACTAAACTTAAATCCAAAAAGACGAAAATGACCCTTAAACCGAAAGGGTGTTTTTGGAAA
1 AAAACACTAAACTTAAATGCAAAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAA
481 TAG
66 TAG
* *
484 AAAACACTAAACTTAAATGCAAAAAGTCAAAAATGACCCTTCGACCGAAA--G-------GGAAA
1 AAAACACTAAACTTAAATGCAAAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAA
540 TAG
66 TAG
* * *
543 AAAACACTAAACTTAAATACAAAAAGATGAAAATGACCCTTCGACCGAAATGGTATTTTTGGAAA
1 AAAACACTAAACTTAAATGCAAAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAA
608 T
66 T
609 GTTTTGATGG
Statistics
Matches: 487, Mismatches: 36, Indels: 19
0.90 0.07 0.04
Matches are distributed among these distances:
59 54 0.11
61 1 0.00
66 1 0.00
67 18 0.04
68 413 0.85
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.21
Consensus pattern (68 bp):
AAAACACTAAACTTAAATGCAAAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAA
TAG
Found at i:568 original size:59 final size:59
Alignment explanation
Indices: 476--592 Score: 200
Period size: 59 Copynumber: 2.0 Consensus size: 59
466 GGGTGTTTTT
*
476 GGAAATAGAAAACACTAAACTTAAATGCAAAAAG-TCAAAAATGACCCTTCGACCGAAAG
1 GGAAATAGAAAACACTAAACTTAAATACAAAAAGAT-AAAAATGACCCTTCGACCGAAAG
*
535 GGAAATAGAAAACACTAAACTTAAATACAAAAAGATGAAAATGACCCTTCGACCGAAA
1 GGAAATAGAAAACACTAAACTTAAATACAAAAAGATAAAAATGACCCTTCGACCGAAA
593 TGGTATTTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
59 54 0.98
60 1 0.02
ACGTcount: A:0.52, C:0.18, G:0.15, T:0.15
Consensus pattern (59 bp):
GGAAATAGAAAACACTAAACTTAAATACAAAAAGATAAAAATGACCCTTCGACCGAAAG
Found at i:4227 original size:22 final size:22
Alignment explanation
Indices: 4199--4240 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
4189 ATAAGCTATG
*
4199 CTAAATGCCAAAATTGAATTTA
1 CTAAATGCCAAAAGTGAATTTA
4221 CTAAATGCCAAAAGTGAATT
1 CTAAATGCCAAAAGTGAATT
4241 AGAAAATGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (22 bp):
CTAAATGCCAAAAGTGAATTTA
Found at i:4802 original size:19 final size:19
Alignment explanation
Indices: 4784--4820 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
4774 ATTTAATTAT
*
4784 TTTA-ATATTATATTTTTA
1 TTTATATATTACATTTTTA
4802 TTTATATATTACATTTTTA
1 TTTATATATTACATTTTTA
4821 CTTAAAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATATATTACATTTTTA
Found at i:5087 original size:2 final size:2
Alignment explanation
Indices: 5080--5107 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5070 TACAAAAATA
5080 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5108 GATAAGTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6639 original size:21 final size:21
Alignment explanation
Indices: 6610--6654 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
6600 AAGACACTGT
* * *
6610 CCACCTGGGTGATCAGGCAAA
1 CCACATGGGTCATCAGACAAA
*
6631 CCACATGGGTCTTCAGACAAA
1 CCACATGGGTCATCAGACAAA
6652 CCA
1 CCA
6655 TGTGGGTGCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.22, T:0.16
Consensus pattern (21 bp):
CCACATGGGTCATCAGACAAA
Found at i:26679 original size:29 final size:28
Alignment explanation
Indices: 26646--26745 Score: 119
Period size: 29 Copynumber: 3.5 Consensus size: 28
26636 AGTACACTTG
*
26646 AAATGACCAAAATGCCCCCTGAACATGAA
1 AAATGACCAAAATG-CCCCTGGACATGAA
* * * *
26675 AAATGACCAAAATGACCCTGGTCCTGGCA
1 AAATGACCAAAATGCCCCTGGACAT-GAA
* *
26704 AAATGACCAAAATGCCCATGGACATGTA
1 AAATGACCAAAATGCCCCTGGACATGAA
26732 AAATGACCAAAATG
1 AAATGACCAAAATG
26746 AGAAGCAAAG
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
28 23 0.38
29 37 0.62
ACGTcount: A:0.43, C:0.24, G:0.17, T:0.16
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTGGACATGAA
Found at i:29568 original size:19 final size:18
Alignment explanation
Indices: 29535--29570 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
29525 TTTAGATAAT
29535 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
29553 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
29571 TAAGTCTTCA
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:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:31131 original size:11 final size:11
Alignment explanation
Indices: 31115--31144 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
31105 ACAACAATGG
31115 ATTTATTTTTT
1 ATTTATTTTTT
31126 ATTTATTTTTT
1 ATTTATTTTTT
31137 ATTT-TTTT
1 ATTTATTTT
31145 ACAGAAATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.21
11 15 0.79
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (11 bp):
ATTTATTTTTT
Found at i:31915 original size:17 final size:18
Alignment explanation
Indices: 31876--31914 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
31866 ATAAAACTTG
*
31876 AAAATTAAAGACATAATT
1 AAAATTAAAGACATAACT
31894 AAAATTAAAG-CATAAACT
1 AAAATTAAAGACAT-AACT
31912 AAA
1 AAA
31915 TAACTAACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.64, C:0.08, G:0.05, T:0.23
Consensus pattern (18 bp):
AAAATTAAAGACATAACT
Found at i:32917 original size:23 final size:22
Alignment explanation
Indices: 32883--32937 Score: 83
Period size: 23 Copynumber: 2.5 Consensus size: 22
32873 TTGCCTTAGC
*
32883 TCTTGTCAACAACTTTGCTTCT
1 TCTTGTCGACAACTTTGCTTCT
32905 TCTTAGTCGACAACTTTGCTTCT
1 TCTT-GTCGACAACTTTGCTTCT
*
32928 CCTTGTCGAC
1 TCTTGTCGAC
32938 TTGCCTCTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 10 0.33
23 20 0.67
ACGTcount: A:0.16, C:0.29, G:0.13, T:0.42
Consensus pattern (22 bp):
TCTTGTCGACAACTTTGCTTCT
Found at i:33366 original size:36 final size:36
Alignment explanation
Indices: 33321--33408 Score: 104
Period size: 36 Copynumber: 2.4 Consensus size: 36
33311 GCAGTGAGGT
** * *
33321 AGCAGCAGGCTGCCTTGCTTGCTGCTCTCACACGGC
1 AGCAGCAGGCTGCCTCACTTGCTACTATCACACGGC
* * *
33357 AGCAGCAGGCTACCTCACTTGCTACTATCACTCGGT
1 AGCAGCAGGCTGCCTCACTTGCTACTATCACACGGC
*
33393 AGCAACAGGCTGCCTC
1 AGCAGCAGGCTGCCTC
33409 GCGGAAGCAG
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.19, C:0.35, G:0.24, T:0.22
Consensus pattern (36 bp):
AGCAGCAGGCTGCCTCACTTGCTACTATCACACGGC
Found at i:39297 original size:46 final size:46
Alignment explanation
Indices: 39230--39338 Score: 218
Period size: 46 Copynumber: 2.4 Consensus size: 46
39220 TTAGATAAAG
39230 CTCTTGATCCAGTGTGAAATATCCCTTTTATTCTTTAAACAATTAC
1 CTCTTGATCCAGTGTGAAATATCCCTTTTATTCTTTAAACAATTAC
39276 CTCTTGATCCAGTGTGAAATATCCCTTTTATTCTTTAAACAATTAC
1 CTCTTGATCCAGTGTGAAATATCCCTTTTATTCTTTAAACAATTAC
39322 CTCTTGATCCAGTGTGA
1 CTCTTGATCCAGTGTGA
39339 TAATTACTCA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 63 1.00
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.40
Consensus pattern (46 bp):
CTCTTGATCCAGTGTGAAATATCCCTTTTATTCTTTAAACAATTAC
Found at i:41993 original size:21 final size:21
Alignment explanation
Indices: 41957--42069 Score: 183
Period size: 21 Copynumber: 5.4 Consensus size: 21
41947 AGCTAGGAGT
41957 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
*
41978 TCAATGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
41999 TCATCGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
42020 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
42041 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
42062 TCATTGGA
1 TCATTGGA
42070 ATTGCCTAAG
Statistics
Matches: 86, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
20 2 0.02
21 84 0.98
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.24
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:43929 original size:25 final size:24
Alignment explanation
Indices: 43893--43939 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
43883 TCCTTCTGTT
43893 CATCTATCATC-AAGTTTTTCATC
1 CATCTATCATCAAAGTTTTTCATC
43916 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATCAAAGTTTTTCA
43940 AATTTTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (24 bp):
CATCTATCATCAAAGTTTTTCATC
Found at i:45596 original size:67 final size:67
Alignment explanation
Indices: 45488--45619 Score: 185
Period size: 67 Copynumber: 2.0 Consensus size: 67
45478 TAATTCTGAA
*
45488 CCTAATTTGAGTGTTGTTTGCAATGACACGAAATCTGTTTTAGATGTTGTTAGTGATGATACAAA
1 CCTAATTTGAGTGTTGTTTGCAATGACACGAAATCTGTTTTAGATGTTGTTAGTGATGAAACAAA
45553 CT
66 CT
** * * * *
45555 CCTAATTT-ATGTGTTGTTTGTGATGACACTAAATCTGTTTTAGGTGTTTTTTGTGATGAAACAA
1 CCTAATTTGA-GTGTTGTTTGCAATGACACGAAATCTGTTTTAGATGTTGTTAGTGATGAAACAA
45619 A
65 A
45620 TTCTGTTTTG
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
66 1 0.02
67 56 0.98
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.42
Consensus pattern (67 bp):
CCTAATTTGAGTGTTGTTTGCAATGACACGAAATCTGTTTTAGATGTTGTTAGTGATGAAACAAA
CT
Found at i:45608 original size:33 final size:33
Alignment explanation
Indices: 45498--45628 Score: 122
Period size: 33 Copynumber: 3.9 Consensus size: 33
45488 CCTAATTTGA
**
45498 GTGTTGTTTGCAATGACACGAAA-TCTGTTTTAG
1 GTGTTGTTTGTGATGACAC-AAACTCTGTTTTAG
* * * ** *
45531 ATGTTGTTAGTGATGATACAAACTCCTAATTTAT
1 GTGTTGTTTGTGATGACACAAACT-CTGTTTTAG
45565 GTGTTGTTTGTGATGACACTAAA-TCTGTTTTAG
1 GTGTTGTTTGTGATGACAC-AAACTCTGTTTTAG
* * *
45598 GTGTTTTTTGTGATGAAACAAATTCTGTTTT
1 GTGTTGTTTGTGATGACACAAACTCTGTTTT
45629 GGATGCTAAT
Statistics
Matches: 78, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
32 6 0.08
33 46 0.59
34 23 0.29
35 3 0.04
ACGTcount: A:0.25, C:0.10, G:0.21, T:0.44
Consensus pattern (33 bp):
GTGTTGTTTGTGATGACACAAACTCTGTTTTAG
Found at i:47500 original size:21 final size:21
Alignment explanation
Indices: 47474--47544 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
47464 TGCTAGGAGT
47474 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
47495 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
47516 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
47537 TCATTGGA
1 TCATTGGA
47545 ATTGCCTAAG
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 2 0.04
21 46 0.96
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:49543 original size:67 final size:67
Alignment explanation
Indices: 49435--49584 Score: 291
Period size: 67 Copynumber: 2.2 Consensus size: 67
49425 ATCAATTAGA
*
49435 GTGGTGAATCTGTATCTCTTGTTGATTTGGGGCTAAAAGAAGCTTGTTCATCTTGTGAATTCCAC
1 GTGGTGAATCTGTATCTCTTGTTGATTTGGGACTAAAAGAAGCTTGTTCATCTTGTGAATTCCAC
49500 TT
66 TT
49502 GTGGTGAATCTGTATCTCTTGTTGATTTGGGACTAAAAGAAGCTTGTTCATCTTGTGAATTCCAC
1 GTGGTGAATCTGTATCTCTTGTTGATTTGGGACTAAAAGAAGCTTGTTCATCTTGTGAATTCCAC
49567 TT
66 TT
49569 GTGGTGAATCTGTATC
1 GTGGTGAATCTGTATC
49585 AAGTTGTGTT
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 82 1.00
ACGTcount: A:0.21, C:0.15, G:0.24, T:0.40
Consensus pattern (67 bp):
GTGGTGAATCTGTATCTCTTGTTGATTTGGGACTAAAAGAAGCTTGTTCATCTTGTGAATTCCAC
TT
Done.