Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012963.1 Corchorus capsularis cultivar CVL-1 contig12984, 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: 20780
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Found at i:6671 original size:17 final size:17
Alignment explanation
Indices: 6649--6682 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
6639 CTCATGATAC
*
6649 CTAGGTAGTATGAGGTG
1 CTAGGTAATATGAGGTG
6666 CTAGGTAATATGAGGTG
1 CTAGGTAATATGAGGTG
6683 ATAAGCTGCA
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:0.26, C:0.06, G:0.38, T:0.29
Consensus pattern (17 bp):
CTAGGTAATATGAGGTG
Found at i:10554 original size:17 final size:17
Alignment explanation
Indices: 10532--10570 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
10522 CTCATGATAC
*
10532 CTAGGTAGTATGAGGTG
1 CTAGGTAATATGAGGTG
10549 CTAGGTAATATGAGGTG
1 CTAGGTAATATGAGGTG
*
10566 ATAGG
1 CTAGG
10571 CTGCATCTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.28, C:0.05, G:0.38, T:0.28
Consensus pattern (17 bp):
CTAGGTAATATGAGGTG
Found at i:11296 original size:155 final size:156
Alignment explanation
Indices: 10916--11298 Score: 402
Period size: 155 Copynumber: 2.5 Consensus size: 156
10906 GAGCTTCTCA
*
10916 CCTCAAATTG-CTCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGCTGAA
1 CCTCAAATTGTC-CTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAACTGAA
** *
10980 ATTTTGCCAAGGAGCTTAGAATATCCACATAAGACTATGGAAAAAATTCTAAGTAAAACCGAGCT
65 ATTTCACCAAGGAGCTTAGAATATCCACATAAGACTATGGAAAAAATTCTAAGTAAAACCGAACT
* * * *
11045 CCCCTTGATGGTGAACTAGGTTTCTCT
130 CCCCTAGATAGAGAACTAGGTTTCACT
* * * * *
11072 CC-CTGAGTTGTCCTTAAATGGAAAACTAGCATAAGTTTTTCATTCTAAGTC-CAACGAAGCTGA
1 CCTC-AAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAA-CTGA
** * * * *
11135 TTTTTCACC-AGTAGACTTAGATTAT-CACCATAAGGCTATGGGAAAAA-TCTAAGTAAAACCGA
64 AATTTCACCAAGGAG-CTTAGAATATCCA-CATAAGACTATGGAAAAAATTCTAAGTAAAACCGA
* * * *
11197 ACT-CTCTAGCATAGAGAAGTTGGTTTGACT
127 ACTCCCCTAG-ATAGAGAACTAGGTTTCACT
* * * ** *
11227 CCTCAAATTGTCCTTAACTGAAAAACTAGCATAAGTTTTTCATGCTAACTCTGTTTGAAATGAAA
1 CCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAACTGAAA
11292 TTTCACC
66 TTTCACC
11299 TAGATGACCT
Statistics
Matches: 183, Mismatches: 36, Indels: 17
0.78 0.15 0.07
Matches are distributed among these distances:
154 4 0.02
155 95 0.52
156 83 0.45
157 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (156 bp):
CCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAACTGAAA
TTTCACCAAGGAGCTTAGAATATCCACATAAGACTATGGAAAAAATTCTAAGTAAAACCGAACTC
CCCTAGATAGAGAACTAGGTTTCACT
Found at i:14170 original size:32 final size:32
Alignment explanation
Indices: 14106--14194 Score: 103
Period size: 32 Copynumber: 2.8 Consensus size: 32
14096 TTTTTTCAGG
*
14106 TTCGGGTTT-GGTTTTTTCGGGTTTC-AGATTT
1 TTCGGGTTTCGGTTTTTTCGAG-TTCGAGATTT
* *
14137 TTCGGGTTTCGATTTTTTCGAGTTCGAGCTTT
1 TTCGGGTTTCGGTTTTTTCGAGTTCGAGATTT
*
14169 TTCGGG-TTCGGGTTTTTTTGAGTTCG
1 TTCGGGTTTC-GGTTTTTTCGAGTTCG
14195 GGTTCAAGTA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
31 15 0.30
32 35 0.70
ACGTcount: A:0.07, C:0.12, G:0.29, T:0.52
Consensus pattern (32 bp):
TTCGGGTTTCGGTTTTTTCGAGTTCGAGATTT
Found at i:14178 original size:16 final size:17
Alignment explanation
Indices: 14106--14176 Score: 71
Period size: 16 Copynumber: 4.5 Consensus size: 17
14096 TTTTTTCAGG
*
14106 TTCGGGTTT-G-GTTTT
1 TTCGGGTTTCGAGATTT
14121 TTCGGGTTTC-AGATTT
1 TTCGGGTTTCGAGATTT
*
14137 TTCGGGTTTCGA-TTTT
1 TTCGGGTTTCGAGATTT
* *
14153 TTCGAG-TTCGAGCTTT
1 TTCGGGTTTCGAGATTT
14169 TTCGGGTT
1 TTCGGGTT
14177 CGGGTTTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
15 14 0.30
16 30 0.65
17 2 0.04
ACGTcount: A:0.07, C:0.13, G:0.28, T:0.52
Consensus pattern (17 bp):
TTCGGGTTTCGAGATTT
Found at i:14185 original size:16 final size:16
Alignment explanation
Indices: 14106--14198 Score: 66
Period size: 16 Copynumber: 5.9 Consensus size: 16
14096 TTTTTTCAGG
*
14106 TTCGGGTT-TGGTTTT
1 TTCGGGTTCGGGTTTT
* *
14121 TTCGGGTTTC-AGATTT
1 TTCGGG-TTCGGGTTTT
*
14137 TTCGGGTTTC-GATTTT
1 TTCGGG-TTCGGGTTTT
* * *
14153 TTCGAGTTCGAGCTTT
1 TTCGGGTTCGGGTTTT
14169 TTCGGGTTCGGGTTTT
1 TTCGGGTTCGGGTTTT
* *
14185 TTTGAGTTCGGGTT
1 TTCGGGTTCGGGTT
14199 CAAGTATTTG
Statistics
Matches: 61, Mismatches: 14, Indels: 5
0.76 0.17 0.06
Matches are distributed among these distances:
15 9 0.15
16 52 0.85
ACGTcount: A:0.06, C:0.12, G:0.30, T:0.52
Consensus pattern (16 bp):
TTCGGGTTCGGGTTTT
Found at i:19513 original size:21 final size:21
Alignment explanation
Indices: 19467--19513 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
19457 GTGACTCGGC
*
19467 ATGGCACGGCATAGGCTCGTG
1 ATGGCACGGCATAGGCGCGTG
* *
19488 GTGGCGCGGCATAGTGCGCG-G
1 ATGGCACGGCATAG-GCGCGTG
19509 ATGGC
1 ATGGC
19514 TTGGCATTGG
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.15, C:0.23, G:0.45, T:0.17
Consensus pattern (21 bp):
ATGGCACGGCATAGGCGCGTG
Done.