Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013731.1 Corchorus capsularis cultivar CVL-1 contig13752, 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: 19289
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:4478 original size:30 final size:30
Alignment explanation
Indices: 4442--4502 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
4432 GTTCATTAGG
4442 AGATCCAAAGAGAATTATTATCAAAGAAAA
1 AGATCCAAAGAGAATTATTATCAAAGAAAA
*
4472 AGATCCAAGGAGAATTATTATCAAAGAAAA
1 AGATCCAAAGAGAATTATTATCAAAGAAAA
4502 A
1 A
4503 AAAATTCAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (30 bp):
AGATCCAAAGAGAATTATTATCAAAGAAAA
Found at i:5166 original size:31 final size:31
Alignment explanation
Indices: 5128--5190 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
5118 GCTCCAATAG
*
5128 GTACTAAACGTTTCAAAATTGGATCAATTTA
1 GTACTAAACCTTTCAAAATTGGATCAATTTA
5159 GTACTAAACCTTTCAAAATTGGATCAATTTA
1 GTACTAAACCTTTCAAAATTGGATCAATTTA
5190 G
1 G
5191 ATTTTTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (31 bp):
GTACTAAACCTTTCAAAATTGGATCAATTTA
Found at i:9022 original size:2 final size:2
Alignment explanation
Indices: 9015--9039 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9005 TTTTAGAAAG
9015 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
9040 TAAAGGTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12234 original size:23 final size:22
Alignment explanation
Indices: 12191--12239 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
12181 GATACATATA
12191 TTTTTTTTATGTTAAAATTTATG
1 TTTTTTTTATGTTAAAATTTA-G
12214 TTTTTTTT-T-TTCAAAATTTTAG
1 TTTTTTTTATGTT-AAAA-TTTAG
12236 TTTT
1 TTTT
12240 ACATATCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 2 0.08
22 10 0.42
23 12 0.50
ACGTcount: A:0.22, C:0.02, G:0.06, T:0.69
Consensus pattern (22 bp):
TTTTTTTTATGTTAAAATTTAG
Found at i:15919 original size:27 final size:27
Alignment explanation
Indices: 15882--15944 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
15872 AAACAAAGTA
15882 ATATTTTAATAGTGGCATAATTA-AAAT
1 ATATTTTAATAGTGGCA-AATTAGAAAT
* * *
15909 ATTTTTTAATATTGGCAATTTAGAAAT
1 ATATTTTAATAGTGGCAAATTAGAAAT
15936 ATATTTTAA
1 ATATTTTAA
15945 AAAATGATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 4 0.13
27 27 0.87
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (27 bp):
ATATTTTAATAGTGGCAAATTAGAAAT
Found at i:16936 original size:350 final size:346
Alignment explanation
Indices: 16289--16985 Score: 972
Period size: 350 Copynumber: 2.0 Consensus size: 346
16279 CAAATTGTCA
* * *
16289 AGCCAGATGTCTTGAAGTCTAAATCTGATATTCTTAAACCCAATTCGTTACTGTGGAAGCACAAA
1 AGCCAGATGTCTTGAAGTCTAAATCTGATATTCTTAAACCCAATTCGTCACTATGGAAGCAAAAA
* * * *
16354 GGAGTCCAAGTCCAATCAGTAATTATGATGCAGTAATTATTCAGCTCTGATGCAACATTGTTAAA
66 GGAGTCCAAGTCCAACCAGTAATTATGATGCAGTAATGATTCAGCCCTAATGCAACATTGTTAAA
* * * * * *
16419 TCCTATTCGAAGGAAGATTTCACAAGAGCAGTTTTTGAAGAAATTTCATAATTTTTTATCTGAAA
131 TCCTATTCAAAAGAAGACTTCACAAGAGCAGTTTTGGAAGAAATTTCATAACTTTTGATCTGAAA
* * * * *
16484 CTCAGAAAAATGCAAATGAGGTACCGTTGGAAAGATGAAACCAAGATTTACAATTTTTATGTTAC
196 CTCAAAAAAATGCAAATGAGGTACCATTGGAAAGAGGAAACCAAGATCTACAACTTTTATGTTAC
** * *
16549 CTTGAGACCTAATCGTGCAGTTCTAGTGGACGATTTTGCCCTTGAAATTTCTAAATAGAATTGAT
261 CTCAAGACCTAATCGTGCAGTTCTAGTGGACGATTTTGCCCTTCAAATTTCTAAACAGAATTGAT
*
16614 CTTCTCCTAAACCGGCTTGGAG
326 CTTCTCCTAAA-CGACTTGGAG
16636 AGCCAGATGTCTTGAAGTCTAAATCTGATATTCTTAAACCCAATTCGTCACTATGGAAGCCCAAA
1 AGCCAGATGTCTTGAAGTCTAAATCTGATATTCTTAAACCCAATTCGTCACTATGGAAG--CAAA
*
16701 CAAGGAGTCCAAGTCCAACCAGTAATTATGATGCAGTAATGATTCAGCCCTAATGCAGCATTGTT
64 -AAGGAGTCCAAGTCCAACCAGTAATTATGATGCAGTAATGATTCAGCCCTAATGCAACATTGTT
*
16766 AAATCCTATTCAAAAG-AGAACTTCACAATAGCAGTTTTGGAAGCAAA-TTCATAACTTTTGATC
128 AAATCCTATTCAAAAGAAG-ACTTCACAAGAGCAGTTTTGGAAG-AAATTTCATAACTTTTGATC
* ***
16829 T-AGAGCTCAAAAAAATGCAAATGAGGTACCATTGGAAAGAGGATTTCAAGATCTACAACTTTTA
191 TGA-AACTCAAAAAAATGCAAATGAGGTACCATTGGAAAGAGGAAACCAAGATCTACAACTTTTA
* * * **
16893 TGTTACCTCAAGACCTAATTC-TGCAGTT-TCGGTGGATGATTTTGCCTTTCAAATTTCTGGACA
255 TGTTACCTCAAGACCTAA-TCGTGCAGTTCT-AGTGGACGATTTTGCCCTTCAAATTTCTAAACA
16956 GAATTGATCTTCTCCTAAACGACTTGGAG
318 GAATTGATCTTCTCCTAAACGACTTGGAG
16985 A
1 A
16986 ATGTTTTGGA
Statistics
Matches: 308, Mismatches: 34, Indels: 14
0.87 0.10 0.04
Matches are distributed among these distances:
347 57 0.19
349 17 0.06
350 229 0.74
351 5 0.02
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (346 bp):
AGCCAGATGTCTTGAAGTCTAAATCTGATATTCTTAAACCCAATTCGTCACTATGGAAGCAAAAA
GGAGTCCAAGTCCAACCAGTAATTATGATGCAGTAATGATTCAGCCCTAATGCAACATTGTTAAA
TCCTATTCAAAAGAAGACTTCACAAGAGCAGTTTTGGAAGAAATTTCATAACTTTTGATCTGAAA
CTCAAAAAAATGCAAATGAGGTACCATTGGAAAGAGGAAACCAAGATCTACAACTTTTATGTTAC
CTCAAGACCTAATCGTGCAGTTCTAGTGGACGATTTTGCCCTTCAAATTTCTAAACAGAATTGAT
CTTCTCCTAAACGACTTGGAG
Found at i:18038 original size:32 final size:32
Alignment explanation
Indices: 18002--18105 Score: 106
Period size: 32 Copynumber: 3.3 Consensus size: 32
17992 TTTATAATAT
* * *
18002 TCTCGGGTTATTCGAGTTTCGGGTCATAT-GGG
1 TCTCGGGTCACTCGAGTTACGGGTCAT-TCGGG
*
18034 TCTCGGGTCACTCGGGTTACGGGTCATTCGGG
1 TCTCGGGTCACTCGAGTTACGGGTCATTCGGG
* *
18066 TTTCGGGTCA-TC-AGGTTACAGGTCATTCGGG
1 TCTCGGGTCACTCGA-GTTACGGGTCATTCGGG
*
18097 TTTCGGGTC
1 TCTCGGGTC
18106 TCGGGTTGGG
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
31 28 0.44
32 35 0.56
ACGTcount: A:0.12, C:0.20, G:0.35, T:0.34
Consensus pattern (32 bp):
TCTCGGGTCACTCGAGTTACGGGTCATTCGGG
Found at i:18050 original size:16 final size:15
Alignment explanation
Indices: 18004--18105 Score: 82
Period size: 16 Copynumber: 6.5 Consensus size: 15
17994 TATAATATTC
* *
18004 TCGGGTTATTCGAGTT
1 TCGGGTCATTCG-GGT
18020 TCGGGTCATAT-GGGT
1 TCGGGTCAT-TCGGGT
*
18035 CTCGGGTCACTCGGGT
1 -TCGGGTCATTCGGGT
18051 TACGGGTCATTCGGGTT
1 T-CGGGTCATTCGGG-T
*
18068 TCGGGTCA-TCAGGT
1 TCGGGTCATTCGGGT
*
18082 TACAGGTCATTCGGGTT
1 T-CGGGTCATTCGGG-T
18099 TCGGGTC
1 TCGGGTC
18106 TCGGGTTGGG
Statistics
Matches: 70, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
14 2 0.03
15 14 0.20
16 49 0.70
17 5 0.07
ACGTcount: A:0.12, C:0.20, G:0.35, T:0.33
Consensus pattern (15 bp):
TCGGGTCATTCGGGT
Found at i:18090 original size:31 final size:32
Alignment explanation
Indices: 18023--18105 Score: 116
Period size: 31 Copynumber: 2.6 Consensus size: 32
18013 TCGAGTTTCG
* * *
18023 GGTCATAT-GGGTCTCGGGTCACTCGGGTTACG
1 GGTCAT-TCGGGTTTCGGGTCACTCAGGTTACA
18055 GGTCATTCGGGTTTCGGGTCA-TCAGGTTACA
1 GGTCATTCGGGTTTCGGGTCACTCAGGTTACA
18086 GGTCATTCGGGTTTCGGGTC
1 GGTCATTCGGGTTTCGGGTC
18106 TCGGGTTGGG
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
31 29 0.62
32 18 0.38
ACGTcount: A:0.12, C:0.20, G:0.36, T:0.31
Consensus pattern (32 bp):
GGTCATTCGGGTTTCGGGTCACTCAGGTTACA
Done.