Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008160.1 Corchorus capsularis cultivar CVL-1 contig08181, 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: 19243
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Found at i:852 original size:1 final size:1
Alignment explanation
Indices: 846--886 Score: 82
Period size: 1 Copynumber: 41.0 Consensus size: 1
836 AGTTCGTGAG
846 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
887 AAAGCTTGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:3869 original size:17 final size:18
Alignment explanation
Indices: 3847--3881 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
3837 GCTTATCACC
3847 TCATACTACCTA-GTACT
1 TCATACTACCTAGGTACT
3864 TCATACTACCTAGGTACT
1 TCATACTACCTAGGTACT
3882 ATGAGAGGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.34
Consensus pattern (18 bp):
TCATACTACCTAGGTACT
Found at i:4049 original size:21 final size:21
Alignment explanation
Indices: 4025--4065 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
4015 CAGAAGAGTT
4025 CGCCTTCCTCAGCAAGTAAAA
1 CGCCTTCCTCAGCAAGTAAAA
4046 CGCCTTCCTCAGCAAGTAAA
1 CGCCTTCCTCAGCAAGTAAA
4066 GCCCACCAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.34, G:0.15, T:0.20
Consensus pattern (21 bp):
CGCCTTCCTCAGCAAGTAAAA
Found at i:4432 original size:55 final size:55
Alignment explanation
Indices: 4277--4440 Score: 222
Period size: 55 Copynumber: 3.0 Consensus size: 55
4267 TCTTATCAAT
* * * * *
4277 CTTCAATGCTGACGCTCGCCTGAGATCTCCGTGAT-TTCCAATGTTCCTTGAAAG
1 CTTCAATGCTGACACTCGCTTGAGATCTTCGTGATCTCCCAGTGTTCCTTGAAAG
* *
4331 CTTCAATGCTGACACACTCGCTTGAGATCTTAGTGATCTCCTAGTGTTCCTTGAAAG
1 CTTCAATGCTG--ACACTCGCTTGAGATCTTCGTGATCTCCCAGTGTTCCTTGAAAG
* *
4388 CTTCAATGCTGATACTCGCTTGAAATCTTCGTGATCTCCCAGTGTTCCTTGAA
1 CTTCAATGCTGACACTCGCTTGAGATCTTCGTGATCTCCCAGTGTTCCTTGAA
4441 GAAAGATTCC
Statistics
Matches: 96, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
54 11 0.11
55 38 0.40
56 20 0.21
57 27 0.28
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (55 bp):
CTTCAATGCTGACACTCGCTTGAGATCTTCGTGATCTCCCAGTGTTCCTTGAAAG
Found at i:12473 original size:6 final size:6
Alignment explanation
Indices: 12462--12488 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
12452 AAAGCAAAGC
12462 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
12489 GCAAATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:19118 original size:22 final size:22
Alignment explanation
Indices: 19069--19118 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
19059 GAAAAAACGG
*
19069 AAAAACATTTTTTTTTTTCGAC
1 AAAAACATTTTTTTTTTTAGAC
**
19091 TCAAACATTTTTTTTTTTTAGA-
1 AAAAACA-TTTTTTTTTTTAGAC
19113 AAAAAC
1 AAAAAC
19119 GGAAAAACAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.36, C:0.12, G:0.04, T:0.48
Consensus pattern (22 bp):
AAAAACATTTTTTTTTTTAGAC
Done.