Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018340.1 Corchorus olitorius cultivar O-4 contig18373, 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: 65341
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:3624 original size:37 final size:38
Alignment explanation
Indices: 3583--3654 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 38
3573 ATGGTGCAAC
* *
3583 ATCATCCTGCACCATAAGATGGTGTAGCAA-TTTAGAA
1 ATCATCCTACACCATAAGATGGTGCAGCAACTTTAGAA
* *
3620 ATCATCCTACACCATAGGGTGGTGCAGCAACTTTA
1 ATCATCCTACACCATAAGATGGTGCAGCAACTTTA
3655 TTTCCTTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 26 0.87
38 4 0.13
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.26
Consensus pattern (38 bp):
ATCATCCTACACCATAAGATGGTGCAGCAACTTTAGAA
Found at i:3827 original size:2 final size:2
Alignment explanation
Indices: 3820--3862 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3810 TCACTCATCT
3820 TA TA TA TA TA TA TA 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 TA TA TA TA
3862 T
1 T
3863 TAGTTTGCCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4785 original size:27 final size:31
Alignment explanation
Indices: 4755--4810 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
4745 CTCATTAAGT
4755 TATTA-CTAGA-A-AAGC-AGTATATATATA
1 TATTAGCTAGAGATAAGCAAGTATATATATA
*
4782 TATTAGCTAGAGATAATCAAGTATATATA
1 TATTAGCTAGAGATAAGCAAGTATATATA
4811 CATAGCTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 5 0.21
28 5 0.21
29 1 0.04
30 3 0.12
31 10 0.42
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.34
Consensus pattern (31 bp):
TATTAGCTAGAGATAAGCAAGTATATATATA
Found at i:10536 original size:25 final size:26
Alignment explanation
Indices: 10498--10549 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
10488 TGTTTACTAT
*
10498 ACAATTTTTTTATGCACTTGAATTAA
1 ACAATTTTTATATGCACTTGAATTAA
*
10524 ACAA-TTTTATATGTACTTGAATTAA
1 ACAATTTTTATATGCACTTGAATTAA
10549 A
1 A
10550 TTATATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (26 bp):
ACAATTTTTATATGCACTTGAATTAA
Found at i:16930 original size:3 final size:3
Alignment explanation
Indices: 16922--16984 Score: 92
Period size: 3 Copynumber: 21.3 Consensus size: 3
16912 TTAATAAGCC
* *
16922 TCT TCT TCT TCT TCT TCT TTT TCT TTT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
16970 TCT T-T TCT TTT TCT T
1 TCT TCT TCT TCT TCT T
16985 GTTTTAGTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (3 bp):
TCT
Found at i:23461 original size:21 final size:21
Alignment explanation
Indices: 23428--23469 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
23418 CCAAACTTCG
* * *
23428 CTCATGGAGCATTAATTATAT
1 CTCAAGGACCATTAATGATAT
23449 CTCAAGGACCATTAATGATAT
1 CTCAAGGACCATTAATGATAT
23470 TGCTGATGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (21 bp):
CTCAAGGACCATTAATGATAT
Found at i:28750 original size:14 final size:13
Alignment explanation
Indices: 28714--28752 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
28704 TATATATTAG
28714 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
28727 TATTTGTTAAATGA
1 AATTTTTTAAAT-A
28741 AATTTTTTAAAT
1 AATTTTTTAAAT
28753 TTTACAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (13 bp):
AATTTTTTAAATA
Found at i:28797 original size:18 final size:18
Alignment explanation
Indices: 28774--28810 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
28764 TTTAGAAATA
28774 AACTTTTACAGTCATTCT
1 AACTTTTACAGTCATTCT
28792 AACTTTTACAGTCATTCT
1 AACTTTTACAGTCATTCT
28810 A
1 A
28811 CTAAAAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.22, G:0.05, T:0.43
Consensus pattern (18 bp):
AACTTTTACAGTCATTCT
Found at i:29023 original size:15 final size:15
Alignment explanation
Indices: 28983--29035 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
28973 TAATTATTCA
*
28983 TTATTT-TTTAAAAC
1 TTATTTATTTAAAAT
* * *
28997 TAATTAAGTTAAAAT
1 TTATTTATTTAAAAT
29012 TTATTTATTTAAAAT
1 TTATTTATTTAAAAT
*
29027 TTAATTATT
1 TTATTTATT
29036 GTGATTAACC
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
14 4 0.13
15 26 0.87
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (15 bp):
TTATTTATTTAAAAT
Found at i:31010 original size:34 final size:34
Alignment explanation
Indices: 30972--31048 Score: 129
Period size: 34 Copynumber: 2.3 Consensus size: 34
30962 GGGTTTGGAG
30972 TCAAACCCCAAACATTTGAAAGTCAAACCACGTT
1 TCAAACCCCAAACATTTGAAAGTCAAACCACGTT
*
31006 TCAAACCCCAAACATTTGAAAGTCAAACCATGTT
1 TCAAACCCCAAACATTTGAAAGTCAAACCACGTT
*
31040 T-TAACCCCA
1 TCAAACCCCA
31049 CTAAAATGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 7 0.17
34 34 0.83
ACGTcount: A:0.40, C:0.30, G:0.08, T:0.22
Consensus pattern (34 bp):
TCAAACCCCAAACATTTGAAAGTCAAACCACGTT
Found at i:31498 original size:21 final size:21
Alignment explanation
Indices: 31465--31566 Score: 114
Period size: 21 Copynumber: 4.9 Consensus size: 21
31455 AACGTGTTGA
* * *
31465 CAAAATTTTGGGTTTGTCTAT
1 CAAACTTTGGGGTTTGACTAT
*
31486 CAAACTTTGGGGTTTGACTTT
1 CAAACTTTGGGGTTTGACTAT
* *
31507 CAAACTATGGGGTTTGACTTT
1 CAAACTTTGGGGTTTGACTAT
*
31528 CAAAATTTGGGGTTTGACTAT
1 CAAACTTTGGGGTTTGACTAT
** *
31549 CATCCTTTGTGGTTTGAC
1 CAAACTTTGGGGTTTGAC
31567 CATGTATGTA
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 69 1.00
ACGTcount: A:0.22, C:0.14, G:0.23, T:0.42
Consensus pattern (21 bp):
CAAACTTTGGGGTTTGACTAT
Found at i:33306 original size:2 final size:2
Alignment explanation
Indices: 33299--33331 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
33289 TTGCTTTGTC
33299 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
33332 CTACATATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33686 original size:42 final size:42
Alignment explanation
Indices: 33627--33706 Score: 151
Period size: 42 Copynumber: 1.9 Consensus size: 42
33617 TAAGGATCAG
33627 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTATAT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTATAT
*
33669 GATTTGAGTTGAGTATTTCTTAATTTATAAAGAATTTT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTT
33707 GAAGACTTAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.33, C:0.04, G:0.15, T:0.49
Consensus pattern (42 bp):
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTATAT
Found at i:35954 original size:43 final size:43
Alignment explanation
Indices: 35888--35977 Score: 171
Period size: 43 Copynumber: 2.1 Consensus size: 43
35878 TTACAATCTT
*
35888 TAAGTGTTGTATATATATGCGGACATGTTTTTGGACATGATAA
1 TAAGTGTTGTATATATATACGGACATGTTTTTGGACATGATAA
35931 TAAGTGTTGTATATATATACGGACATGTTTTTGGACATGATAA
1 TAAGTGTTGTATATATATACGGACATGTTTTTGGACATGATAA
35974 TAAG
1 TAAG
35978 GAGGATGTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.32, C:0.07, G:0.22, T:0.39
Consensus pattern (43 bp):
TAAGTGTTGTATATATATACGGACATGTTTTTGGACATGATAA
Found at i:44522 original size:12 final size:12
Alignment explanation
Indices: 44505--44530 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
44495 GTTTTTCTTT
44505 GTCATATATACG
1 GTCATATATACG
44517 GTCATATATACG
1 GTCATATATACG
44529 GT
1 GT
44531 TTTTTCTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (12 bp):
GTCATATATACG
Found at i:45935 original size:103 final size:103
Alignment explanation
Indices: 45809--46015 Score: 405
Period size: 103 Copynumber: 2.0 Consensus size: 103
45799 TGCAAGAATC
45809 AGAATTTTACACAATTGACAGATTCTATTGAGCAGAGGGACTCAATTGACACCAAATTGTGGTAG
1 AGAATTTTACACAATTGACAGATTCTATTGAGCAGAGGGACTCAATTGACACCAAATTGTGGTAG
*
45874 AGGGACCAAATTGACAATTTTCGTAGTAGGGGTGCCAA
66 AGGGACCAAATTGACAATTTTCGTAGTAGAGGTGCCAA
45912 AGAATTTTACACAATTGACAGATTCTATTGAGCAGAGGGACTCAATTGACACCAAATTGTGGTAG
1 AGAATTTTACACAATTGACAGATTCTATTGAGCAGAGGGACTCAATTGACACCAAATTGTGGTAG
45977 AGGGACCAAATTGACAATTTTCGTAGTAGAGGTGCCAA
66 AGGGACCAAATTGACAATTTTCGTAGTAGAGGTGCCAA
46015 A
1 A
46016 TTGATCCCTC
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 103 1.00
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (103 bp):
AGAATTTTACACAATTGACAGATTCTATTGAGCAGAGGGACTCAATTGACACCAAATTGTGGTAG
AGGGACCAAATTGACAATTTTCGTAGTAGAGGTGCCAA
Found at i:47359 original size:36 final size:36
Alignment explanation
Indices: 47312--47386 Score: 123
Period size: 36 Copynumber: 2.1 Consensus size: 36
47302 CAGTCTTATT
** *
47312 ATCTGTTATTCGGCTAAAATTAGTGATAAGAGAAAG
1 ATCTGTTATTCGGAAAAAAATAGTGATAAGAGAAAG
47348 ATCTGTTATTCGGAAAAAAATAGTGATAAGAGAAAG
1 ATCTGTTATTCGGAAAAAAATAGTGATAAGAGAAAG
47384 ATC
1 ATC
47387 GGTTTGATGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.43, C:0.08, G:0.21, T:0.28
Consensus pattern (36 bp):
ATCTGTTATTCGGAAAAAAATAGTGATAAGAGAAAG
Found at i:48641 original size:13 final size:13
Alignment explanation
Indices: 48623--48659 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
48613 GTTTATAAGT
48623 ACTTAAGATTAAC
1 ACTTAAGATTAAC
*
48636 ACTTAAGATTAGC
1 ACTTAAGATTAAC
48649 ACTTAAGATTA
1 ACTTAAGATTA
48660 TTTGGCCTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (13 bp):
ACTTAAGATTAAC
Found at i:50348 original size:18 final size:18
Alignment explanation
Indices: 50308--50348 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
50298 ACACATGTCC
* *
50308 ATTTCCTGAATTAATTTT
1 ATTTTCTGAATTAATTGT
*
50326 TTTTTCTGAATTAATTGT
1 ATTTTCTGAATTAATTGT
50344 ATTTT
1 ATTTT
50349 TTTTTATTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.61
Consensus pattern (18 bp):
ATTTTCTGAATTAATTGT
Found at i:56178 original size:31 final size:31
Alignment explanation
Indices: 56143--56203 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
56133 CTCCAAATTT
56143 CAAATCCCTAATTGTTTCTCAGCAATGGTTC
1 CAAATCCCTAATTGTTTCTCAGCAATGGTTC
56174 CAAATCCCTAATTGTTTCTCAGCAATGGTT
1 CAAATCCCTAATTGTTTCTCAGCAATGGTT
56204 TCTGATGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.36
Consensus pattern (31 bp):
CAAATCCCTAATTGTTTCTCAGCAATGGTTC
Found at i:56523 original size:24 final size:24
Alignment explanation
Indices: 56466--56524 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
56456 GATTAGTGCC
**
56466 ATGCTTGAGCTGATTTGATATTTG
1 ATGCTTGAATTGATTTGATATTTG
*
56490 ATGATTGAATTGATTTGATATTTG
1 ATGCTTGAATTGATTTGATATTTG
56514 ATGCTTGAATT
1 ATGCTTGAATT
56525 TATGAGTATG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.25, C:0.05, G:0.22, T:0.47
Consensus pattern (24 bp):
ATGCTTGAATTGATTTGATATTTG
Found at i:59137 original size:46 final size:46
Alignment explanation
Indices: 59083--59174 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
59073 CGAGAAAATT
59083 ACCCGACTCATTTGAGCTAAACCTTGATGACCCGAACCCGAAACCC
1 ACCCGACTCATTTGAGCTAAACCTTGATGACCCGAACCCGAAACCC
*
59129 ACCCGACTCATTTGAGTTAAACCTTGATGACCCGAACCCGAAACCC
1 ACCCGACTCATTTGAGCTAAACCTTGATGACCCGAACCCGAAACCC
59175 GTCCAACCTG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.30, C:0.36, G:0.15, T:0.18
Consensus pattern (46 bp):
ACCCGACTCATTTGAGCTAAACCTTGATGACCCGAACCCGAAACCC
Found at i:59771 original size:22 final size:22
Alignment explanation
Indices: 59745--59791 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
59735 CTTTTAGTTG
*
59745 AGTAAAACT-ATAAAAGTAAAAT
1 AGTAAAA-TGATAAAAATAAAAT
*
59767 AGTAAAATGGTAAAAATAAAAT
1 AGTAAAATGATAAAAATAAAAT
59789 AGT
1 AGT
59792 TATAAGGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.62, C:0.02, G:0.13, T:0.23
Consensus pattern (22 bp):
AGTAAAATGATAAAAATAAAAT
Found at i:59783 original size:93 final size:95
Alignment explanation
Indices: 59669--59853 Score: 284
Period size: 93 Copynumber: 2.0 Consensus size: 95
59659 GCTTTTAATT
* * * *
59669 AAATAAGTAATATCGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAAT-AAAAGTAG
1 AAATAAGTAAAATCGTAAAAATAAAATAGGTATAAGGATATAAGATTTAATAAAATAAAAAATAG
*
59733 AGCTTTTAGTTGAGTAAAACTATAAAAGTA
66 AGCTTTTAGTTGACTAAAACTATAAAAGTA
* *
59763 AAAT-AGTAAAATGGTAAAAATAAAATAGTTATAAGGATATAAGATTTAATAAAATAAAAAATAG
1 AAATAAGTAAAATCGTAAAAATAAAATAGGTATAAGGATATAAGATTTAATAAAATAAAAAATAG
*
59827 AGTTTTTAGTTGACTAAAACTATAAAA
66 AGCTTTTAGTTGACTAAAACTATAAAA
59854 ATTTAAACAA
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
93 46 0.56
94 36 0.44
ACGTcount: A:0.54, C:0.03, G:0.14, T:0.30
Consensus pattern (95 bp):
AAATAAGTAAAATCGTAAAAATAAAATAGGTATAAGGATATAAGATTTAATAAAATAAAAAATAG
AGCTTTTAGTTGACTAAAACTATAAAAGTA
Found at i:59931 original size:31 final size:31
Alignment explanation
Indices: 59889--59950 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
59879 ATATTCGAAA
*
59889 AATAAGGGTATAATAGACGATTAAAAAGTTT
1 AATAAGAGTATAATAGACGATTAAAAAGTTT
* * *
59920 AATAAGAGTATAATAGGCGATTCAAGAGTTT
1 AATAAGAGTATAATAGACGATTAAAAAGTTT
59951 TACAAAACTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.29
Consensus pattern (31 bp):
AATAAGAGTATAATAGACGATTAAAAAGTTT
Found at i:62201 original size:24 final size:24
Alignment explanation
Indices: 62169--62224 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
62159 TTGGCTGTCG
*
62169 TTGCAATCTTGGATTTGATTGAGA
1 TTGCAATCTTGGATTTGACTGAGA
*
62193 TTGCAATCTTGGATTTGACTGAGG
1 TTGCAATCTTGGATTTGACTGAGA
*
62217 TTGGAATC
1 TTGCAATC
62225 CTCTACTTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.23, C:0.11, G:0.27, T:0.39
Consensus pattern (24 bp):
TTGCAATCTTGGATTTGACTGAGA
Done.