Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013155.1 Corchorus capsularis cultivar CVL-1 contig13176, 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: 42905
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Found at i:853 original size:11 final size:11
Alignment explanation
Indices: 837--868 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
827 GAAGTTCGTG
837 TTTGAAGATTA
1 TTTGAAGATTA
*
848 TTTGAAGATAA
1 TTTGAAGATTA
859 TTTGAAGATT
1 TTTGAAGATT
869 TGTAGATCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (11 bp):
TTTGAAGATTA
Found at i:7425 original size:11 final size:11
Alignment explanation
Indices: 7409--7438 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
7399 AAAGTTCGTG
*
7409 TTTGAAGATTA
1 TTTGAAGATAA
7420 TTTGAAGATAA
1 TTTGAAGATAA
7431 TTTGAAGA
1 TTTGAAGA
7439 ATTGAAGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (11 bp):
TTTGAAGATAA
Found at i:7445 original size:19 final size:18
Alignment explanation
Indices: 7421--7459 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
7411 TGAAGATTAT
*
7421 TTGAAGATAATTTGAAGAA
1 TTGAAGACAA-TTGAAGAA
*
7440 TTGAAGACCATTGAAGAA
1 TTGAAGACAATTGAAGAA
7458 TT
1 TT
7460 ATTTCAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.31
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAA
Found at i:19852 original size:15 final size:16
Alignment explanation
Indices: 19823--19852 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19813 GTGTGAAGTC
19823 AAATTGATCTTTTGAA
1 AAATTGATCTTTTGAA
19839 AAATTGAT-TTTTGA
1 AAATTGATCTTTTGA
19853 TTAACTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47
Consensus pattern (16 bp):
AAATTGATCTTTTGAA
Found at i:22916 original size:30 final size:30
Alignment explanation
Indices: 22882--22946 Score: 130
Period size: 30 Copynumber: 2.2 Consensus size: 30
22872 TATTTCATTA
22882 GCACATCTATTTAGTCATCACACTTATGAG
1 GCACATCTATTTAGTCATCACACTTATGAG
22912 GCACATCTATTTAGTCATCACACTTATGAG
1 GCACATCTATTTAGTCATCACACTTATGAG
22942 GCACA
1 GCACA
22947 CAACACACAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.31
Consensus pattern (30 bp):
GCACATCTATTTAGTCATCACACTTATGAG
Found at i:36405 original size:21 final size:20
Alignment explanation
Indices: 36366--36407 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
36356 TCATTTGCTT
*
36366 ATTGTCTTCAATGCTCTTCA
1 ATTGTCTTCAATGCACTTCA
*
36386 ATTGATCTTCAATGGACTTCA
1 ATTG-TCTTCAATGCACTTCA
36407 A
1 A
36408 ACCTTCAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.40
Consensus pattern (20 bp):
ATTGTCTTCAATGCACTTCA
Found at i:39092 original size:30 final size:31
Alignment explanation
Indices: 39058--39132 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 31
39048 CCGGTTGTGC
** *
39058 CCGGTCTTGTGCGATTGGC-CCATGCCATGG
1 CCGGTCTTGTGCGATTCCCTCCATGCAATGG
* *
39088 CCGGTCATGTGCGA-TCCCTCCATGTAATGG
1 CCGGTCTTGTGCGATTCCCTCCATGCAATGG
39118 CCGGTCTTGTGCGAT
1 CCGGTCTTGTGCGAT
39133 GGCTTCCTCT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
29 2 0.05
30 35 0.95
ACGTcount: A:0.12, C:0.29, G:0.31, T:0.28
Consensus pattern (31 bp):
CCGGTCTTGTGCGATTCCCTCCATGCAATGG
Found at i:42566 original size:21 final size:21
Alignment explanation
Indices: 42540--42579 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
42530 ACCATGGACG
*
42540 AGACAGATACATAAATGAAAA
1 AGACAGATACAGAAATGAAAA
*
42561 AGACAGATTCAGAAATGAA
1 AGACAGATACAGAAATGAA
42580 GAAGTTCAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.10, G:0.17, T:0.15
Consensus pattern (21 bp):
AGACAGATACAGAAATGAAAA
Done.