Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011105.1 Corchorus capsularis cultivar CVL-1 contig11126, 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: 58907
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:5439 original size:14 final size:14
Alignment explanation
Indices: 5422--5449 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5412 GGAACAGAGG
5422 AAATGTCAAAGCTT
1 AAATGTCAAAGCTT
5436 AAATGTCAAAGCTT
1 AAATGTCAAAGCTT
5450 GCCTAGCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (14 bp):
AAATGTCAAAGCTT
Found at i:12292 original size:31 final size:31
Alignment explanation
Indices: 12256--12315 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
12246 TACCTTTTAT
*
12256 AGACAAATAAGTCTCTTCATAATTGTTCATA
1 AGACAAATAAGACTCTTCATAATTGTTCATA
* *
12287 AGACAAATAAGACTTTTCATAGTTGTTCA
1 AGACAAATAAGACTCTTCATAATTGTTCA
12316 CTTATGAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (31 bp):
AGACAAATAAGACTCTTCATAATTGTTCATA
Found at i:13411 original size:31 final size:32
Alignment explanation
Indices: 13363--13424 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 32
13353 CATCATAGTG
13363 ATATAACTCTTTTGTTTCTCTAAGAAACCAAC
1 ATATAACTCTTTTGTTTCTCTAAGAAACCAAC
* *
13395 ATATATCTC-TTTGTTTCTTTAAGAAACCAA
1 ATATAACTCTTTTGTTTCTCTAAGAAACCAA
13425 GACACTCCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 20 0.71
32 8 0.29
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.40
Consensus pattern (32 bp):
ATATAACTCTTTTGTTTCTCTAAGAAACCAAC
Found at i:14659 original size:37 final size:37
Alignment explanation
Indices: 14615--14685 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
14605 CTTGATCAAC
* *
14615 ATACATGTCTTTTCATATAGACATAACTTTATGATCA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGATCA
14652 ATACATGTCTTTCCAAATAGACATAACTTTATGA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGA
14686 ATAATTATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (37 bp):
ATACATGTCTTTCCAAATAGACATAACTTTATGATCA
Found at i:14750 original size:31 final size:31
Alignment explanation
Indices: 14714--14773 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
14704 TACCTTTTAT
14714 AGACAAATAAGACTCTTCATAATTGTTCATA
1 AGACAAATAAGACTCTTCATAATTGTTCATA
* *
14745 AGACAAATAAGTCTCTTCATAGTTGTTCA
1 AGACAAATAAGACTCTTCATAATTGTTCA
14774 CTTATGAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (31 bp):
AGACAAATAAGACTCTTCATAATTGTTCATA
Found at i:31348 original size:13 final size:13
Alignment explanation
Indices: 31330--31354 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31320 ATTAAGGAGC
31330 AAGAAAAGAAAGA
1 AAGAAAAGAAAGA
31343 AAGAAAAGAAAG
1 AAGAAAAGAAAG
31355 CAAATTCATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAGAAAAGAAAGA
Found at i:39650 original size:18 final size:18
Alignment explanation
Indices: 39629--39678 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
39619 AGGCAACGGC
*
39629 GGCAGCGGAGGCAGCCGT
1 GGCAGCGGAGGCAGACGT
* * *
39647 GGCATCGGTGGCAAACGT
1 GGCAGCGGAGGCAGACGT
*
39665 GGCAGCGGGGGCAG
1 GGCAGCGGAGGCAG
39679 TCTCCAAGGT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.18, C:0.24, G:0.50, T:0.08
Consensus pattern (18 bp):
GGCAGCGGAGGCAGACGT
Found at i:42426 original size:5 final size:5
Alignment explanation
Indices: 42418--42442 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
42408 CAACATTATA
42418 AAAAC AAAAC AAAAC AAAAC AAAAC
1 AAAAC AAAAC AAAAC AAAAC AAAAC
42443 TCTAAAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:45212 original size:3 final size:3
Alignment explanation
Indices: 45199--45230 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
45189 TATTATATAT
45199 ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
45231 TACTACAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:48193 original size:15 final size:15
Alignment explanation
Indices: 48173--48208 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
48163 ATGGATAATA
48173 CAAAATGAATAAATG
1 CAAAATGAATAAATG
48188 CAAAATGAATAAATG
1 CAAAATGAATAAATG
48203 CAAAAT
1 CAAAAT
48209 TCATTCAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.61, C:0.08, G:0.11, T:0.19
Consensus pattern (15 bp):
CAAAATGAATAAATG
Found at i:51650 original size:19 final size:20
Alignment explanation
Indices: 51626--51683 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 20
51616 TTGTTTAACA
51626 ACTGTACAGATGAGATTA-C
1 ACTGTACAGATGAGATTAGC
* *
51645 ACTGTACAGATTAGATTAGGT
1 ACTGTACAGATGAGATTA-GC
*
51666 ACTTTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
51684 TTAGAGCAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (20 bp):
ACTGTACAGATGAGATTAGC
Done.