Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014011.1 Corchorus capsularis cultivar CVL-1 contig14032, 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: 31964
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:9097 original size:25 final size:25
Alignment explanation
Indices: 9076--9222 Score: 231
Period size: 25 Copynumber: 5.9 Consensus size: 25
9066 GGTAAACGCT
* *
9076 CATGTTCTTGCGTTTGGCAAACGAG
1 CATGTACTTGCGTTTAGCAAACGAG
* *
9101 CCTGTGCTTGCGTTTAGCAAACGAG
1 CATGTACTTGCGTTTAGCAAACGAG
9126 CATGTACTTGCGTTTAGCAAACGAG
1 CATGTACTTGCGTTTAGCAAACGAG
9151 CATGTACTTGCGTTTAGCAAACGAG
1 CATGTACTTGCGTTTAGCAAACGAG
9176 CATGTACTTGCGTTTAGCAAACGAG
1 CATGTACTTGCGTTTAGCAAACGAG
* * *
9201 CCTGTGCTTGCGTTTAGAAAAC
1 CATGTACTTGCGTTTAGCAAAC
9223 ACATAGGCTA
Statistics
Matches: 114, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 114 1.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.29
Consensus pattern (25 bp):
CATGTACTTGCGTTTAGCAAACGAG
Found at i:12500 original size:20 final size:20
Alignment explanation
Indices: 12477--12515 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
12467 ACTGGCGGGC
12477 TTTACTTGCTGAGGAAGGCA
1 TTTACTTGCTGAGGAAGGCA
12497 TTTACTTGCTGAGGAAGGC
1 TTTACTTGCTGAGGAAGGC
12516 GAACTCTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (20 bp):
TTTACTTGCTGAGGAAGGCA
Found at i:12701 original size:17 final size:17
Alignment explanation
Indices: 12663--12695 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
12653 CTCATGATAC
12663 CTAGGTAGTATGAGGTA
1 CTAGGTAGTATGAGGTA
12680 CTAGGTAGTATGAGGT
1 CTAGGTAGTATGAGGT
12696 GATAGGCTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.06, G:0.36, T:0.30
Consensus pattern (17 bp):
CTAGGTAGTATGAGGTA
Found at i:13236 original size:156 final size:155
Alignment explanation
Indices: 13050--13411 Score: 432
Period size: 156 Copynumber: 2.3 Consensus size: 155
13040 CTTCTCACCC
*
13050 CAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATG-AGCTGAAACT
1 CAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAACGAAGCTG--A-T
**
13114 TTTCCA-AGGT-ACTTAGAATATTTCCATAAGACTAT-GGAAAAAATTCTAAGTAAAACCGAACT
63 TTTCCACA-GTAACTTAGAATATCACCATAAGACTATGGGAAAAAA-TCTAAGTAAAACCGAACT
* * * *
13176 CCCCTTG-ATTGTGAACTAGGTTTCTCTCC-
126 -CCCTAGAATAGAGAACTAGGTTTCACTCCT
* ** *
13205 CTGAGTTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTC-CAACGAAGCTGATTT
1 C-AAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAACGAAGCTGATTT
* *
13269 TCCACCAGTAGACTTAGATTATCACCATAAGACTATGGGAAAAAATCTAAGTAAAACCGAACTCT
65 TCCA-CAGTA-ACTTAGAATATCACCATAAGACTATGGGAAAAAATCTAAGTAAAACCGAACTCC
* * *
13334 CTAGAATAGAGAAGTTGGTTTGACTCCT
128 CTAGAATAGAGAACTAGGTTTCACTCCT
* *
13362 CAAACTGTCCTTAACTGAAAAACTAGCATAAGTTTTTCATACTAAGTCTG
1 CAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTG
13412 TTTGAGATGA
Statistics
Matches: 175, Mismatches: 22, Indels: 18
0.81 0.10 0.08
Matches are distributed among these distances:
153 7 0.04
154 3 0.02
155 9 0.05
156 147 0.84
157 9 0.05
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (155 bp):
CAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAACGAAGCTGATTTT
CCACAGTAACTTAGAATATCACCATAAGACTATGGGAAAAAATCTAAGTAAAACCGAACTCCCTA
GAATAGAGAACTAGGTTTCACTCCT
Found at i:14905 original size:30 final size:31
Alignment explanation
Indices: 14839--14905 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 31
14829 GGACAGGTCA
* *
14839 CAAAAAAGTATAAAATTGAGAGTTTATGAGG
1 CAAAAACGTATAAAATTGAAAGTTTATGAGG
*
14870 C-AAAACGTTTAAAATT-AAAGTTTATGAGG
1 CAAAAACGTATAAAATTGAAAGTTTATGAGG
14899 CAAAAAC
1 CAAAAAC
14906 ATTTGAACTG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 13 0.41
30 18 0.56
31 1 0.03
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.25
Consensus pattern (31 bp):
CAAAAACGTATAAAATTGAAAGTTTATGAGG
Found at i:15334 original size:20 final size:20
Alignment explanation
Indices: 15311--15352 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
15301 TTTCTTCTAT
15311 TTTAATTACTTGCAA-TTTAG
1 TTTAATTA-TTGCAACTTTAG
*
15331 TTTAATTATTTCAACTTTAG
1 TTTAATTATTGCAACTTTAG
15351 TT
1 TT
15353 CATAGTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.29, C:0.10, G:0.07, T:0.55
Consensus pattern (20 bp):
TTTAATTATTGCAACTTTAG
Found at i:23978 original size:21 final size:21
Alignment explanation
Indices: 23952--23991 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
23942 ACCAAAGTTA
23952 TCTTCATCATCAAGTAAATGG
1 TCTTCATCATCAAGTAAATGG
23973 TCTTCATCATCAAGTAAAT
1 TCTTCATCATCAAGTAAAT
23992 ATTATGATCA
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:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (21 bp):
TCTTCATCATCAAGTAAATGG
Found at i:28714 original size:1 final size:1
Alignment explanation
Indices: 28708--28735 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
28698 TAATATTTAT
28708 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
28736 CTTTTCATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:29186 original size:25 final size:25
Alignment explanation
Indices: 29158--29214 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
29148 TACCTTTGGA
29158 TATTAAATTACTAAAATCCCCTAAT
1 TATTAAATTACTAAAATCCCCTAAT
29183 TATTAAATTACTAAAATCCCCTAAT
1 TATTAAATTACTAAAATCCCCTAAT
29208 TATTAAA
1 TATTAAA
29215 CCGGAGCATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.37
Consensus pattern (25 bp):
TATTAAATTACTAAAATCCCCTAAT
Found at i:30717 original size:29 final size:30
Alignment explanation
Indices: 30680--30746 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
30670 TTCACTTTTG
*
30680 AAACGTAAGGAATTAATTTGTACCAA-A-AA
1 AAACATAAGGAATTAATTTGT-CCAAGACAA
* *
30709 AAACATAAGGGATTATTTTGTCCAAGACAA
1 AAACATAAGGAATTAATTTGTCCAAGACAA
30739 AAACATAA
1 AAACATAA
30747 ACGATTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 4 0.12
29 19 0.58
30 10 0.30
ACGTcount: A:0.51, C:0.12, G:0.13, T:0.24
Consensus pattern (30 bp):
AAACATAAGGAATTAATTTGTCCAAGACAA
Found at i:30823 original size:20 final size:19
Alignment explanation
Indices: 30795--30833 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
30785 AATATACAAT
30795 GTAAAAAGTTAAAGAAAAAA
1 GTAAAAAG-TAAAGAAAAAA
* *
30815 GTAATAAGTCAAGAAAAAA
1 GTAAAAAGTAAAGAAAAAA
30834 AAAATGTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.67, C:0.03, G:0.15, T:0.15
Consensus pattern (19 bp):
GTAAAAAGTAAAGAAAAAA
Found at i:31641 original size:90 final size:90
Alignment explanation
Indices: 31487--31845 Score: 682
Period size: 90 Copynumber: 4.0 Consensus size: 90
31477 CGTCGCAATT
* *
31487 GCTGAACTTTGAGATGTTGCCTAAAGGTGTGCCAATTCCTCCATCGGGGCCAAGCACTCGGACAT
1 GCTGAACTTTCAGATGTTGCCTAAAGGTGTGCCGATTCCTCCATCGGGGCCAAGCACTCGGACAT
31552 CAGCAGATGTTCCACCACCTCCTTC
66 CAGCAGATGTTCCACCACCTCCTTC
*
31577 TCTGAACTTTCAGATGTTGCCTAAAGGTGTGCCGATTCCTCCATCGGGGCCAAGCACTCGGACAT
1 GCTGAACTTTCAGATGTTGCCTAAAGGTGTGCCGATTCCTCCATCGGGGCCAAGCACTCGGACAT
31642 CAGCAGATGTTCCACCACCTCCTTC
66 CAGCAGATGTTCCACCACCTCCTTC
31667 GCTGAACTTTCAGATGTTGCCTAAAGGTGTGCCGATTCCTCCATCGGGGCCAAGCACTCGGACAT
1 GCTGAACTTTCAGATGTTGCCTAAAGGTGTGCCGATTCCTCCATCGGGGCCAAGCACTCGGACAT
31732 CAGCAGATGTTCCACCACCTCCTTC
66 CAGCAGATGTTCCACCACCTCCTTC
31757 GCTGAACTTTCAGATGTTGCCTAAAGGGTGTGCCGATTCCTCCATCGGGGCCAAGCACTCGGACA
1 GCTGAACTTTCAGATGTTGCCTAAA-GGTGTGCCGATTCCTCCATCGGGGCCAAGCACTCGGACA
31822 TCAGCAGATGTTCCACCACCTCCT
65 TCAGCAGATGTTCCACCACCTCCT
31846 ATGCTAGCCT
Statistics
Matches: 264, Mismatches: 4, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
90 201 0.76
91 63 0.24
ACGTcount: A:0.21, C:0.32, G:0.22, T:0.25
Consensus pattern (90 bp):
GCTGAACTTTCAGATGTTGCCTAAAGGTGTGCCGATTCCTCCATCGGGGCCAAGCACTCGGACAT
CAGCAGATGTTCCACCACCTCCTTC
Done.