Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023633.1 Corchorus olitorius cultivar O-4 contig23666, 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: 27047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:2847 original size:16 final size:17
Alignment explanation
Indices: 2815--2847 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2805 GATCGAACGA
2815 AACAAAATAAAAGATAG
1 AACAAAATAAAAGATAG
*
2832 AACAAATTAAAA-ATAG
1 AACAAAATAAAAGATAG
2848 TAATTAAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.70, C:0.06, G:0.09, T:0.15
Consensus pattern (17 bp):
AACAAAATAAAAGATAG
Found at i:10096 original size:26 final size:28
Alignment explanation
Indices: 10066--10125 Score: 97
Period size: 29 Copynumber: 2.2 Consensus size: 28
10056 TTTTAATTTG
10066 ATTATTTGAAC-AT-ATAGAGATATCTT
1 ATTATTTGAACAATAATAGAGATATCTT
10092 ATTATTTGAACATATAATAGAGATATCTT
1 ATTATTTGAACA-ATAATAGAGATATCTT
10121 ATTAT
1 ATTAT
10126 AGTAACGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
26 11 0.35
28 2 0.06
29 18 0.58
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (28 bp):
ATTATTTGAACAATAATAGAGATATCTT
Found at i:11899 original size:14 final size:13
Alignment explanation
Indices: 11880--11918 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
11870 TATTCCAAAC
*
11880 AAAAAATAAAAAG
1 AAAAAAAAAAAAG
11893 TAAAAAAAAAAAAG
1 -AAAAAAAAAAAAG
11907 AAAAAGAAAAAA
1 AAAAA-AAAAAA
11919 CAGGAAGGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 5 0.22
14 18 0.78
ACGTcount: A:0.87, C:0.00, G:0.08, T:0.05
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:11905 original size:20 final size:19
Alignment explanation
Indices: 11880--11918 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
11870 TATTCCAAAC
*
11880 AAAAAATAAAAAGTAAAAAA
1 AAAAAAGAAAAAG-AAAAAA
11900 AAAAAAGAAAAAGAAAAAA
1 AAAAAAGAAAAAGAAAAAA
11919 CAGGAAGGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.87, C:0.00, G:0.08, T:0.05
Consensus pattern (19 bp):
AAAAAAGAAAAAGAAAAAA
Found at i:14936 original size:24 final size:24
Alignment explanation
Indices: 14882--14936 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
14872 ATCAGGAAAT
*
14882 TTTTCAACTAGATTTTTGTTTTTG
1 TTTTAAACTAGATTTTTGTTTTTG
***
14906 AGGTAAACTAGATTTTTGTTTTTG
1 TTTTAAACTAGATTTTTGTTTTTG
14930 TTTTAAA
1 TTTTAAA
14937 AATAATAAAT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.05, G:0.15, T:0.56
Consensus pattern (24 bp):
TTTTAAACTAGATTTTTGTTTTTG
Found at i:20347 original size:17 final size:17
Alignment explanation
Indices: 20325--20359 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
20315 CTTGTCTTTA
20325 TATTTGCTT-TTGTGTTT
1 TATTTGCTTATT-TGTTT
20342 TATTTGCTTATTTGTTT
1 TATTTGCTTATTTGTTT
20359 T
1 T
20360 TATGTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.88
18 2 0.12
ACGTcount: A:0.09, C:0.06, G:0.14, T:0.71
Consensus pattern (17 bp):
TATTTGCTTATTTGTTT
Found at i:20770 original size:21 final size:21
Alignment explanation
Indices: 20731--20770 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
20721 ATTTTTCAAG
* *
20731 AAAATTTTAAATTTTTTTTTT
1 AAAATTTTAAACTTCTTTTTT
*
20752 AAAATTTTATACTTCTTTT
1 AAAATTTTAAACTTCTTTT
20771 CCTTTGATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (21 bp):
AAAATTTTAAACTTCTTTTTT
Found at i:22540 original size:122 final size:121
Alignment explanation
Indices: 22140--22683 Score: 611
Period size: 122 Copynumber: 4.5 Consensus size: 121
22130 TTCAAACTTA
* * * * **
22140 TCAAATTC-ATTTAAGGATTTACTTAAATCTTAAAGGAATTATGAAAGTTTCCCAAAGGGTTTAT
1 TCAAATTCGA-TTAAGGATTCACTTAAATCTT-AATGAATTATGAAA-CTTACCAAAAAGTTT-T
* * * * *
22204 TAACTGAAGGTTTTAATTACTTAATTAAATCTTAAGTTTT-AGGTTACTTAACCTT-GATT
62 AAACTCAAGGTTTTAATTACTTAATTAAACCTAAAGTTTTAAGGTCACTTAACCTTAG-TT
* *
22263 TCAAGTTCGATTAAGGATTCACTTAAATCTTAATGAATTATGAAAC-T-CC-CAAA-TTTTATTA
1 TCAAATTCGATTAAGGATTCACTTAAATCTTAATGAATTATGAAACTTACCAAAAAGTTTTA--A
* * * *
22324 ACT-ATAGGTTATAATCACTTAATTAAACCTAAAGTTTTAAGGTCACTTGACTTTCA-TT
64 ACTCA-AGGTTTTAATTACTTAATTAAACCTAAAGTTTTAAGGTCACTTAACCTT-AGTT
** * * * *
22382 TCCGATTTGATTAAGGATTTACTTAAATCTTAATGAATTATGATACTTACCAAAAACTTTTAAAC
1 TCAAATTCGATTAAGGATTCACTTAAATCTTAATGAATTATGAAACTTACCAAAAAGTTTTAAAC
* * * *
22447 TCAAGGTTTTGATTACTTAATTAAACCCAATGTTTTAAGGTGACTTAACCTTAGTTT
66 TCAAGGTTTTAATTACTTAATTAAACCTAAAGTTTTAAGGTCACTTAACCTTAG-TT
* *
22504 TTAAATTCGATTAAGGATTCACTTAAATCTTAATGAATTATGAAATTTACCAAAAAGGTTTTAAA
1 TCAAATTCGATTAAGGATTCACTTAAATCTTAATGAATTATGAAACTTACCAAAAA-GTTTTAAA
22569 CTCAAGGTTTTAATTACTTAATTAAACCTAAAGTTTTAAGGTCACTTAACCTTAGTT
65 CTCAAGGTTTTAATTACTTAATTAAACCTAAAGTTTTAAGGTCACTTAACCTTAGTT
* * * * *
22626 TCAAATTCAATTAAGGATTCACCTAAATCTTAATAAAATAGTGAAAATTACCAAAAAG
1 TCAAATTCGATTAAGGATTCACTTAAATCTTAATGAATTA-TGAAACTTACCAAAAAG
22684 GGATTAATTC
Statistics
Matches: 357, Mismatches: 48, Indels: 33
0.82 0.11 0.08
Matches are distributed among these distances:
116 1 0.00
117 4 0.01
118 34 0.10
119 56 0.16
120 3 0.01
121 47 0.13
122 106 0.30
123 105 0.29
124 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (121 bp):
TCAAATTCGATTAAGGATTCACTTAAATCTTAATGAATTATGAAACTTACCAAAAAGTTTTAAAC
TCAAGGTTTTAATTACTTAATTAAACCTAAAGTTTTAAGGTCACTTAACCTTAGTT
Found at i:22610 original size:123 final size:122
Alignment explanation
Indices: 22140--22684 Score: 610
Period size: 123 Copynumber: 4.5 Consensus size: 122
22130 TTCAAACTTA
* * * *
22140 TCAAATTC-ATTTAAGGATTTACTTAAATCTTAAAGGAATTATGAAAGTTT-CCCAAAGGGTTTA
1 TCAAATTCGA-TTAAGGATTCACTTAAATCTT-AATGAATTATGAAA-TTTACCAAAAAGGTTT-
* * * * *
22203 TTAACTGAAGGTTTTAATTACTTAATTAAATCTTAAGTTTT-AGGTTACTTAACCTT-GATT
62 TAAACTCAAGGTTTTAATTACTTAATTAAACCTAAAGTTTTAAGGTCACTTAACCTTAG-TT
* * *
22263 TCAAGTTCGATTAAGGATTCACTTAAATCTTAATGAATTATGAAA-CT-CC-CAAA--TTTTATT
1 TCAAATTCGATTAAGGATTCACTTAAATCTTAATGAATTATGAAATTTACCAAAAAGGTTTTA--
* * * *
22323 AACT-ATAGGTTATAATCACTTAATTAAACCTAAAGTTTTAAGGTCACTTGACTTTCA-TT
64 AACTCA-AGGTTTTAATTACTTAATTAAACCTAAAGTTTTAAGGTCACTTAACCTT-AGTT
** * * * * *
22382 TCCGATTTGATTAAGGATTTACTTAAATCTTAATGAATTATGATACTTACCAAAAA-CTTTTAAA
1 TCAAATTCGATTAAGGATTCACTTAAATCTTAATGAATTATGAAATTTACCAAAAAGGTTTTAAA
* * * *
22446 CTCAAGGTTTTGATTACTTAATTAAACCCAATGTTTTAAGGTGACTTAACCTTAGTTT
66 CTCAAGGTTTTAATTACTTAATTAAACCTAAAGTTTTAAGGTCACTTAACCTTAG-TT
*
22504 TTAAATTCGATTAAGGATTCACTTAAATCTTAATGAATTATGAAATTTACCAAAAAGGTTTTAAA
1 TCAAATTCGATTAAGGATTCACTTAAATCTTAATGAATTATGAAATTTACCAAAAAGGTTTTAAA
22569 CTCAAGGTTTTAATTACTTAATTAAACCTAAAGTTTTAAGGTCACTTAACCTTAGTT
66 CTCAAGGTTTTAATTACTTAATTAAACCTAAAGTTTTAAGGTCACTTAACCTTAGTT
* * * * *
22626 TCAAATTCAATTAAGGATTCACCTAAATCTTAATAAAATAGTGAAAATTACCAAAAAGG
1 TCAAATTCGATTAAGGATTCACTTAAATCTTAATGAATTA-TGAAATTTACCAAAAAGG
22685 GATTAATTCT
Statistics
Matches: 358, Mismatches: 48, Indels: 32
0.82 0.11 0.07
Matches are distributed among these distances:
116 1 0.00
117 4 0.01
118 33 0.09
119 55 0.15
120 5 0.01
121 47 0.13
122 105 0.29
123 107 0.30
124 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.38
Consensus pattern (122 bp):
TCAAATTCGATTAAGGATTCACTTAAATCTTAATGAATTATGAAATTTACCAAAAAGGTTTTAAA
CTCAAGGTTTTAATTACTTAATTAAACCTAAAGTTTTAAGGTCACTTAACCTTAGTT
Found at i:23416 original size:29 final size:29
Alignment explanation
Indices: 23374--23438 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
23364 GAAGCTCACA
23374 GAAACGATGATTTAGCCCTGGAATTTGTC
1 GAAACGATGATTTAGCCCTGGAATTTGTC
23403 GAAACGATGATTTAGCCCTGGAATTTGTC
1 GAAACGATGATTTAGCCCTGGAATTTGTC
*
23432 AAAACGA
1 GAAACGA
23439 CGTCATTTCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (29 bp):
GAAACGATGATTTAGCCCTGGAATTTGTC
Done.