Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010835.1 Corchorus capsularis cultivar CVL-1 contig10856, 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: 41279
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:7118 original size:2 final size:2
Alignment explanation
Indices: 7113--7164 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
7103 ATATATATAT
7113 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
7155 AG AG AG AG AG
1 AG AG AG AG AG
7165 TACTCTAATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:7256 original size:6 final size:6
Alignment explanation
Indices: 7245--7274 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
7235 TGGGACGTAA
7245 AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG
1 AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG
7275 CGATCCAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (6 bp):
AGAGGG
Found at i:7659 original size:23 final size:25
Alignment explanation
Indices: 7619--7665 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
7609 TTAATTAAGC
*
7619 AGTTAAATCATTAATTATCTATAGT
1 AGTTAAATCATTAATTATATATAGT
7644 AGTTAAA-C-TTAATTATATATAG
1 AGTTAAATCATTAATTATATATAG
7666 CACTGCACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 13 0.62
24 1 0.05
25 7 0.33
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (25 bp):
AGTTAAATCATTAATTATATATAGT
Found at i:9870 original size:5 final size:5
Alignment explanation
Indices: 9860--9884 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
9850 CATTTCCATG
9860 GAGAT GAGAT GAGAT GAGAT GAGAT
1 GAGAT GAGAT GAGAT GAGAT GAGAT
9885 AGTAATAAGT
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:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (5 bp):
GAGAT
Found at i:11110 original size:1 final size:1
Alignment explanation
Indices: 11070--11097 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
11060 ATCAGTTAAG
11070 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
11098 CCTTTTCTTT
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:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:15656 original size:1 final size:1
Alignment explanation
Indices: 15650--15687 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
15640 TCTTTGGTTC
15650 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
15688 ACAATTATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:26107 original size:20 final size:20
Alignment explanation
Indices: 26071--26108 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
26061 AAAGCAGATG
*
26071 AAATTACCTTTTTCTTGTCT
1 AAATTACCTTTTCCTTGTCT
26091 AAATT-CCTTGTTCCTTGT
1 AAATTACCTT-TTCCTTGT
26109 TGAAGACCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.18, C:0.21, G:0.08, T:0.53
Consensus pattern (20 bp):
AAATTACCTTTTCCTTGTCT
Found at i:27312 original size:18 final size:19
Alignment explanation
Indices: 27285--27332 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
27275 AACAAATGAG
*
27285 TGAAAATGAAACTC-AAAC
1 TGAAAGTGAAACTCAAAAC
*
27303 TGAAAGTGAAACTCAAAAG
1 TGAAAGTGAAACTCAAAAC
27322 TGAAAGTGAAA
1 TGAAAGTGAAA
27333 TGAATCACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.54, C:0.10, G:0.19, T:0.17
Consensus pattern (19 bp):
TGAAAGTGAAACTCAAAAC
Found at i:27409 original size:6 final size:6
Alignment explanation
Indices: 27398--27431 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
27388 GTCAGCTCAG
27398 CTACAA CTACAA CTACAAA CTACAA CTACAA CTA
1 CTACAA CTACAA CTAC-AA CTACAA CTACAA CTA
27432 GAGCATCCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (6 bp):
CTACAA
Found at i:27420 original size:13 final size:13
Alignment explanation
Indices: 27398--27428 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
27388 GTCAGCTCAG
27398 CTAC-AACTACAA
1 CTACAAACTACAA
27410 CTACAAACTACAA
1 CTACAAACTACAA
27423 CTACAA
1 CTACAA
27429 CTAGAGCATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (13 bp):
CTACAAACTACAA
Done.