Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007350.1 Corchorus capsularis cultivar CVL-1 contig07371, 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: 40433
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:1706 original size:79 final size:79
Alignment explanation
Indices: 1575--1812 Score: 458
Period size: 79 Copynumber: 3.0 Consensus size: 79
1565 AAAAGACAGA
1575 TGTCAACTCCTAAACCCCGCTTGTGTAATCTACCAAACTACACTGACAGTGTAAGTATAATTTTA
1 TGTCAACTCCTAAACCCCGCTTGTGTAATCTACCAAACTACACTGACAGTGTAAGTATAATTTTA
*
1640 CGGATGTCAACGGG
66 GGGATGTCAACGGG
1654 TGTCAACTCCTAAACCCCGCTTGTGTAATCTACCAAACTACACTGACAGTGTAAGTATAATTTTA
1 TGTCAACTCCTAAACCCCGCTTGTGTAATCTACCAAACTACACTGACAGTGTAAGTATAATTTTA
1719 GGGATGTCAACGGG
66 GGGATGTCAACGGG
*
1733 TGTCAACTCCTAAACCCCGCTTGTATAATCTACCAAACTACACTGACAGTGTAAGTATAATTTTA
1 TGTCAACTCCTAAACCCCGCTTGTGTAATCTACCAAACTACACTGACAGTGTAAGTATAATTTTA
1798 GGGATGTCAACGGG
66 GGGATGTCAACGGG
1812 T
1 T
1813 AGGGTATACG
Statistics
Matches: 157, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 157 1.00
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (79 bp):
TGTCAACTCCTAAACCCCGCTTGTGTAATCTACCAAACTACACTGACAGTGTAAGTATAATTTTA
GGGATGTCAACGGG
Found at i:2133 original size:19 final size:18
Alignment explanation
Indices: 2104--2145 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
2094 TGAGTAGTTT
*
2104 TTAAGTAAAAATATAATA
1 TTAAATAAAAATATAATA
*
2122 TATAAATAAAAATGTAATA
1 T-TAAATAAAAATATAATA
2141 TTAAA
1 TTAAA
2146 ACAATTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (18 bp):
TTAAATAAAAATATAATA
Found at i:2445 original size:37 final size:37
Alignment explanation
Indices: 2395--2466 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
2385 AAAAATTGTC
*
2395 TCCAATTATGTCAATAGTACAAAGTAGAATTATTGAT
1 TCCAATTATGTCAATAGTAAAAAGTAGAATTATTGAT
2432 TCCAATTATGTCAATAGTAAAAAGTAGAATTATTG
1 TCCAATTATGTCAATAGTAAAAAGTAGAATTATTG
2467 TATTTGTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.35
Consensus pattern (37 bp):
TCCAATTATGTCAATAGTAAAAAGTAGAATTATTGAT
Found at i:2968 original size:24 final size:25
Alignment explanation
Indices: 2936--2986 Score: 95
Period size: 24 Copynumber: 2.1 Consensus size: 25
2926 AAAAGATCTT
2936 CATACTTTCTTCCAATTATATT-TC
1 CATACTTTCTTCCAATTATATTCTC
2960 CATACTTTCTTCCAATTATATTCTC
1 CATACTTTCTTCCAATTATATTCTC
2985 CA
1 CA
2987 ATATTTATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.25, C:0.27, G:0.00, T:0.47
Consensus pattern (25 bp):
CATACTTTCTTCCAATTATATTCTC
Found at i:2997 original size:24 final size:24
Alignment explanation
Indices: 2936--2998 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 24
2926 AAAAGATCTT
*
2936 CATACTTTCTTCCAATTATATTTC
1 CATACTTTCATCCAATTATATTTC
*
2960 CATACTTTCTTCCAATTATATTCTC
1 CATACTTTCATCCAATTATATT-TC
2985 CAATA-TTT-ATCCAA
1 C-ATACTTTCATCCAA
2999 ACTTTACTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
24 27 0.75
25 6 0.17
26 3 0.08
ACGTcount: A:0.29, C:0.25, G:0.00, T:0.46
Consensus pattern (24 bp):
CATACTTTCATCCAATTATATTTC
Found at i:5162 original size:18 final size:18
Alignment explanation
Indices: 5139--5174 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5129 CCTATGAAAT
*
5139 TCCAAAAAATTTTCAAAA
1 TCCAAAAAATCTTCAAAA
5157 TCCAAAAAATCTTCAAAA
1 TCCAAAAAATCTTCAAAA
5175 AACATTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.19, G:0.00, T:0.25
Consensus pattern (18 bp):
TCCAAAAAATCTTCAAAA
Found at i:10333 original size:21 final size:21
Alignment explanation
Indices: 10309--10354 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
10299 TTCAAAAAAA
10309 AAAGGAAAAATAATGGTCTGC
1 AAAGGAAAAATAATGGTCTGC
10330 AAAGGAAAAATAATGGTCTGC
1 AAAGGAAAAATAATGGTCTGC
10351 AAAG
1 AAAG
10355 TTATCCCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.50, C:0.09, G:0.24, T:0.17
Consensus pattern (21 bp):
AAAGGAAAAATAATGGTCTGC
Found at i:10750 original size:24 final size:25
Alignment explanation
Indices: 10720--10774 Score: 103
Period size: 24 Copynumber: 2.2 Consensus size: 25
10710 AAATAAAAGA
10720 TCTCCATACTTTCTTCCAATTATAT
1 TCTCCATACTTTCTTCCAATTATAT
10745 T-TCCATACTTTCTTCCAATTATAT
1 TCTCCATACTTTCTTCCAATTATAT
10769 TCTCCA
1 TCTCCA
10775 ATCTTTATCC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 24 0.83
25 5 0.17
ACGTcount: A:0.24, C:0.29, G:0.00, T:0.47
Consensus pattern (25 bp):
TCTCCATACTTTCTTCCAATTATAT
Found at i:10785 original size:24 final size:24
Alignment explanation
Indices: 10722--10786 Score: 80
Period size: 24 Copynumber: 2.7 Consensus size: 24
10712 ATAAAAGATC
*
10722 TCCATACTTTCTTCCAATTATATT
1 TCCATACTTTCATCCAATTATATT
*
10746 TCCATACTTTCTTCCAATTATATT
1 TCCATACTTTCATCCAATTATATT
10770 CTCCA-ATCTTT-ATCCAA
1 -TCCATA-CTTTCATCCAA
10787 ACTTTACTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
24 30 0.79
25 8 0.21
ACGTcount: A:0.26, C:0.28, G:0.00, T:0.46
Consensus pattern (24 bp):
TCCATACTTTCATCCAATTATATT
Found at i:11019 original size:6 final size:6
Alignment explanation
Indices: 11008--11038 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
10998 TCATTAATGT
11008 TTAGGG TTAGGG TTAGGG TTTAGGG TTAGGG
1 TTAGGG TTAGGG TTAGGG -TTAGGG TTAGGG
11039 AGAGGTGCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.16, C:0.00, G:0.48, T:0.35
Consensus pattern (6 bp):
TTAGGG
Found at i:11032 original size:13 final size:12
Alignment explanation
Indices: 11008--11038 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
10998 TCATTAATGT
11008 TTAGGGTTAGGG
1 TTAGGGTTAGGG
11020 TTAGGGTTTAGGG
1 TTAGGG-TTAGGG
11033 TTAGGG
1 TTAGGG
11039 AGAGGTGCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.16, C:0.00, G:0.48, T:0.35
Consensus pattern (12 bp):
TTAGGGTTAGGG
Found at i:11123 original size:16 final size:17
Alignment explanation
Indices: 11092--11124 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
11082 TTGTAAACAC
11092 AAGTTGAGTTGATTAATA
1 AAGTTGAG-TGATTAATA
11110 AAGTTGAG-GATTAAT
1 AAGTTGAGTGATTAAT
11125 TTTCCCAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.36
Consensus pattern (17 bp):
AAGTTGAGTGATTAATA
Found at i:14106 original size:21 final size:21
Alignment explanation
Indices: 14082--14121 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
14072 AACTGGTGGA
14082 TTTTACTTGCTGAGGAAGGTG
1 TTTTACTTGCTGAGGAAGGTG
14103 TTTTACTTGCTGAGGAAGG
1 TTTTACTTGCTGAGGAAGG
14122 CGAACTCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.10, G:0.33, T:0.38
Consensus pattern (21 bp):
TTTTACTTGCTGAGGAAGGTG
Found at i:18286 original size:24 final size:24
Alignment explanation
Indices: 18250--18299 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
18240 TTCTGAGTAC
*
18250 TTTGCAACGGAATCAAAAACGGAA
1 TTTGCAACAGAATCAAAAACGGAA
*
18274 TTTGCAATAGAATCAAAAACGGAA
1 TTTGCAACAGAATCAAAAACGGAA
18298 TT
1 TT
18300 CTATCTGACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.14, G:0.18, T:0.22
Consensus pattern (24 bp):
TTTGCAACAGAATCAAAAACGGAA
Found at i:21579 original size:21 final size:19
Alignment explanation
Indices: 21549--21591 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
21539 ATCTAGAGAA
*
21549 AATAATAAATATTCAAATATT
1 AATAAAAAAT-TTCAAA-ATT
*
21570 AATAAAAAATTTCTAAATT
1 AATAAAAAATTTCAAAATT
21589 AAT
1 AAT
21592 GTTAAAATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 6 0.30
20 5 0.25
21 9 0.45
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
AATAAAAAATTTCAAAATT
Found at i:21772 original size:99 final size:98
Alignment explanation
Indices: 21651--22040 Score: 507
Period size: 99 Copynumber: 3.9 Consensus size: 98
21641 TTTATTAAGT
*
21651 TTATTATC-ATGTGGAAGCGGATTTAGACACGGCTATGTAGTTTCCGTGTTAAATTCCGTTT-CA
1 TTATTATCAAT-TGGAAGCGGATTTAGACACGGATATGTAGTTTCCGTGTTAAATTCCGTTTCCA
**
21714 AATGAAATAAAAAAATTTATTTATAGAATAATTTTT
65 AATGAAAT-AAAAAATTTATTTATAGAAT-ATTTAC
* * * * *
21750 TTATCATCAATTAGAAGCGGATTTAGACACGCATATGTAGTTTCCGTGTTAAATTTCGCTTCCAA
1 TTATTATCAATTGGAAGCGGATTTAGACACGGATATGTAGTTTCCGTGTTAAATTCCGTTTCCAA
*
21815 ATGAAATAGAAAATTTATTTATAGAAT-TTAGTAC
66 ATGAAATAAAAAATTTATTTATAGAATATT--TAC
**
21849 TTATTATCGGTTGGAAGCGGATTTAGACACGGATATGTAGTTTCCGTGTTAAATTCCGTTTCCAA
1 TTATTATCAATTGGAAGCGGATTTAGACACGGATATGTAGTTTCCGTGTTAAATTCCGTTTCCAA
* * * *
21914 ATGGAATAAAAACTTTATTTATGGATTATATTAC
66 ATGAAATAAAAAATTTATTTATAGAATAT-TTAC
* * * *
21948 ATATTATCATTTGGAAGCAGATTTAGACACGGATATGTAGTTTCCGTGTTAAATTTCGTTTCCAA
1 TTATTATCAATTGGAAGCGGATTTAGACACGGATATGTAGTTTCCGTGTTAAATTCCGTTTCCAA
**
22013 ATGAAATAAAAAAAAATATTTATAGAAT
66 ATGAAAT-AAAAAATTTATTTATAGAAT
22041 TTAGTGCTCA
Statistics
Matches: 252, Mismatches: 32, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
97 2 0.01
99 221 0.88
100 28 0.11
101 1 0.00
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.37
Consensus pattern (98 bp):
TTATTATCAATTGGAAGCGGATTTAGACACGGATATGTAGTTTCCGTGTTAAATTCCGTTTCCAA
ATGAAATAAAAAATTTATTTATAGAATATTTAC
Found at i:21989 original size:198 final size:199
Alignment explanation
Indices: 21662--22045 Score: 576
Period size: 198 Copynumber: 1.9 Consensus size: 199
21652 TATTATCATG
*
21662 TGGAAGCGGATTTAGACACGGCTATGTAGTTTCCGTGTTAAATTCCGTTTCAAATGAAATAAAAA
1 TGGAAGCGGATTTAGACACGGATATGTAGTTTCCGTGTTAAATTCCGTTTCAAATGAAATAAAAA
*** *
21727 AATTTATTTATAGAATAATTTTTTTATCATCAATTAGAAGCGGATTTAGACACGCATATGTAGTT
66 AATTTATTTATAGAATAATTTACATATCATCAATTAGAAGCAGATTTAGACACGCATATGTAGTT
* **
21792 TCCGTGTTAAATTTCGCTTCCAAATGAAAT-AGAAAATTTATTTATAGAATTTAGTACTTATTAT
131 TCCGTGTTAAATTTCGCTTCCAAATGAAATAAAAAAAAATATTTATAGAATTTAGTACTTATTAT
21856 CGGT
196 CGGT
*
21860 TGGAAGCGGATTTAGACACGGATATGTAGTTTCCGTGTTAAATTCCGTTTCCAAATGGAAT-AAA
1 TGGAAGCGGATTTAGACACGGATATGTAGTTTCCGTGTTAAATTCCGTTT-CAAATGAAATAAAA
* * * * * * *
21924 AACTTTATTTAT-GGATTATATTACATATTATCATTTGGAAGCAGATTTAGACACGGATATGTAG
65 AAATTTATTTATAGAATAAT-TTACATATCATCAATTAGAAGCAGATTTAGACACGCATATGTAG
*
21988 TTTCCGTGTTAAATTTCGTTTCCAAATGAAATAAAAAAAAATATTTATAGAATTTAGT
129 TTTCCGTGTTAAATTTCGCTTCCAAATGAAATAAAAAAAAATATTTATAGAATTTAGT
22046 GCTCATCTTC
Statistics
Matches: 166, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
197 5 0.03
198 130 0.78
199 31 0.19
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (199 bp):
TGGAAGCGGATTTAGACACGGATATGTAGTTTCCGTGTTAAATTCCGTTTCAAATGAAATAAAAA
AATTTATTTATAGAATAATTTACATATCATCAATTAGAAGCAGATTTAGACACGCATATGTAGTT
TCCGTGTTAAATTTCGCTTCCAAATGAAATAAAAAAAAATATTTATAGAATTTAGTACTTATTAT
CGGT
Found at i:22428 original size:16 final size:16
Alignment explanation
Indices: 22407--22438 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
22397 TGCTTCGTTT
*
22407 GCTTCATCGCTTTCAC
1 GCTTCATCACTTTCAC
22423 GCTTCATCACTTTCAC
1 GCTTCATCACTTTCAC
22439 TGAAAGTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.38, G:0.09, T:0.38
Consensus pattern (16 bp):
GCTTCATCACTTTCAC
Found at i:32314 original size:21 final size:21
Alignment explanation
Indices: 32290--32330 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
32280 ACTGGTGGGC
32290 TTTACTTGCTGAGGAAGGCGT
1 TTTACTTGCTGAGGAAGGCGT
32311 TTTACTTGCTGAGGAAGGCG
1 TTTACTTGCTGAGGAAGGCG
32331 AACTCTTCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.15, G:0.34, T:0.32
Consensus pattern (21 bp):
TTTACTTGCTGAGGAAGGCGT
Found at i:33393 original size:21 final size:21
Alignment explanation
Indices: 33367--33419 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
33357 GCACTGGAGT
* *
33367 ACATGGGGCGCGAGGCAAACC
1 ACATGGGGCGCCAAGCAAACC
* *
33388 ACATGGGGTGCCAAGCAAGCC
1 ACATGGGGCGCCAAGCAAACC
33409 ACAT-GGGCGCC
1 ACATGGGGCGCC
33420 CAGCGCTAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 6 0.22
21 21 0.78
ACGTcount: A:0.26, C:0.30, G:0.36, T:0.08
Consensus pattern (21 bp):
ACATGGGGCGCCAAGCAAACC
Found at i:35230 original size:17 final size:17
Alignment explanation
Indices: 35205--35238 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
35195 CACCCTTCTT
35205 GAAAATTCAAAAATTCA
1 GAAAATTCAAAAATTCA
*
35222 GAAACTTCAAAAATTCA
1 GAAAATTCAAAAATTCA
35239 TAGCCGATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.15, G:0.06, T:0.24
Consensus pattern (17 bp):
GAAAATTCAAAAATTCA
Found at i:35324 original size:10 final size:9
Alignment explanation
Indices: 35311--35345 Score: 52
Period size: 10 Copynumber: 3.7 Consensus size: 9
35301 AGTTATATCG
35311 AAAAATATAA
1 AAAAATA-AA
35321 AAAAATAAA
1 AAAAATAAA
35330 ATAAAATAAA
1 A-AAAATAAA
35340 AAAAAT
1 AAAAAT
35346 TTTCGACCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (9 bp):
AAAAATAAA
Done.