Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004010.1 Corchorus capsularis cultivar CVL-1 contig04018, 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: 32476
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Found at i:7805 original size:60 final size:60
Alignment explanation
Indices: 7737--7869 Score: 171
Period size: 60 Copynumber: 2.2 Consensus size: 60
7727 GCTAATTGCT
** * * *
7737 CAAATAAGGGTTTAACGTTTGTCAAAATGGTCAAATAAGTG-TCTGATC-TTTTAATCTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAG-GATCCGATCATTTT-ATCTGGC
* *
7797 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGATCCGATCATTTTATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGATCCGATCATTTTATCTGGC
7857 CAAATAAGGGCCT
1 CAAATAAGGGCCT
7870 GACATCGAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
59 1 0.02
60 59 0.92
61 4 0.06
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.31
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGATCCGATCATTTTATCTGGC
Found at i:8334 original size:20 final size:18
Alignment explanation
Indices: 8309--8348 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 18
8299 TTCCCTAATG
8309 TGTAATTATTTTATTTGACT
1 TGTAATTATTTT-TTTG-CT
8329 TGTAATTATTTTTTTGCT
1 TGTAATTATTTTTTTGCT
8347 TG
1 TG
8349 ATAAATGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 4 0.20
19 4 0.20
20 12 0.60
ACGTcount: A:0.20, C:0.05, G:0.12, T:0.62
Consensus pattern (18 bp):
TGTAATTATTTTTTTGCT
Found at i:9681 original size:13 final size:13
Alignment explanation
Indices: 9663--9697 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
9653 ATTTCTTTGA
9663 TTTTTTTATGGGT
1 TTTTTTTATGGGT
*
9676 TTTTTTTATGGTT
1 TTTTTTTATGGGT
9689 TCTTTTTTA
1 T-TTTTTTA
9698 CCGTTGTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.09, C:0.03, G:0.14, T:0.74
Consensus pattern (13 bp):
TTTTTTTATGGGT
Found at i:23631 original size:19 final size:19
Alignment explanation
Indices: 23590--23633 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
23580 TTATCCCTCT
*
23590 TCTCTCTACCCCCACTAAG
1 TCTCTCTACCCCCACTAAC
*
23609 TCTCTCT-CCTCCCACTCAC
1 TCTCTCTACC-CCCACTAAC
23628 TCTCTC
1 TCTCTC
23634 ATAGTCAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 2 0.09
19 20 0.91
ACGTcount: A:0.14, C:0.52, G:0.02, T:0.32
Consensus pattern (19 bp):
TCTCTCTACCCCCACTAAC
Found at i:24237 original size:21 final size:21
Alignment explanation
Indices: 24203--24263 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
24193 CCGATGAGAG
*
24203 TAAAAT-TGGTTACTGTACATA
1 TAAAATGT-GTTACTGTACAGA
* * * *
24224 TTACATTTGTTACTGTAGAGA
1 TAAAATGTGTTACTGTACAGA
24245 TAAAATGTGTTACTGTACA
1 TAAAATGTGTTACTGTACA
24264 AATGAGAATA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.39
Consensus pattern (21 bp):
TAAAATGTGTTACTGTACAGA
Found at i:27481 original size:2 final size:2
Alignment explanation
Indices: 27476--27513 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
27466 AACCAGATGA
*
27476 CT CT CT CT TT CT CT CT C- CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
27514 CACTGCACCA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:30245 original size:62 final size:63
Alignment explanation
Indices: 30148--30286 Score: 226
Period size: 62 Copynumber: 2.2 Consensus size: 63
30138 CAGTGTTGTC
* * **
30148 TGAAGTTCCATGTGGTAGTCCTTCGCCTTTTGCTTTTTCTGTATTCAAAATTTC-AATATATG
1 TGAAGTTCCATGTGGTAGTCCTTCGCCTTTTGCTTTTCCCGTATTCAAAACATCTAATATATG
*
30210 TGAAGTTCCATGTGGTAGTCCTTTGCCTTTTGCTTTTCCCGTATTCAAAACATCTAATATATG
1 TGAAGTTCCATGTGGTAGTCCTTCGCCTTTTGCTTTTCCCGTATTCAAAACATCTAATATATG
30273 TGAAGTTCCATGTG
1 TGAAGTTCCATGTG
30287 AAGGCAATCT
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
62 49 0.69
63 22 0.31
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.42
Consensus pattern (63 bp):
TGAAGTTCCATGTGGTAGTCCTTCGCCTTTTGCTTTTCCCGTATTCAAAACATCTAATATATG
Done.