Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008637.1 Corchorus capsularis cultivar CVL-1 contig08658, 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: 25756
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1161 original size:40 final size:41
Alignment explanation
Indices: 1103--1183 Score: 105
Period size: 40 Copynumber: 2.0 Consensus size: 41
1093 TTTATAACTA
*
1103 GGGGCTAAATCTAGATTTAATTT-TTTACC-TTAATTATTAG
1 GGGGCTAAACCTAGATTTAATTTATTT-CCTTTAATTATTAG
1143 GGGGCTAAACCT-GAATTTAATTTATTTCCTTTTAATTATTA
1 GGGGCTAAACCTAG-ATTTAATTTATTTCC-TTTAATTATTA
1184 TGAGGGTCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
39 1 0.03
40 22 0.61
41 3 0.08
42 10 0.28
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (41 bp):
GGGGCTAAACCTAGATTTAATTTATTTCCTTTAATTATTAG
Found at i:16686 original size:69 final size:69
Alignment explanation
Indices: 16608--16773 Score: 287
Period size: 69 Copynumber: 2.4 Consensus size: 69
16598 TATTTCTTTG
* * * * *
16608 ATGTGACAACTTCAAGTGTCATTAATATGTTTGATGTGACAACTTCAGGTGCCACTAATATTCTT
1 ATGTGACAACTTCAGGTGCCACTAATATGCTTGATGTGACAACTTCAAGTGCCACTAATATTCTT
16673 GATC
66 GATC
16677 ATGTGACAACTTCAGGTGCCACTAATATGCTTGATGTGACAACTTCAAGTGCCACTAATATTCTT
1 ATGTGACAACTTCAGGTGCCACTAATATGCTTGATGTGACAACTTCAAGTGCCACTAATATTCTT
16742 GATC
66 GATC
16746 ATGTGACAACTTCAGGTGCCACTAATAT
1 ATGTGACAACTTCAGGTGCCACTAATAT
16774 ATAAGGTAGT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 92 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (69 bp):
ATGTGACAACTTCAGGTGCCACTAATATGCTTGATGTGACAACTTCAAGTGCCACTAATATTCTT
GATC
Found at i:16687 original size:36 final size:33
Alignment explanation
Indices: 16605--16773 Score: 223
Period size: 33 Copynumber: 4.9 Consensus size: 33
16595 TACTATTTCT
* * *
16605 TTGATGTGACAACTTCAAGTGTCATTAATATGT-
1 TTGATGTGACAACTTCAGGTGCCACTAATAT-TC
16638 TTGATGTGACAACTTCAGGTGCCACTAATATTC
1 TTGATGTGACAACTTCAGGTGCCACTAATATTC
*
16671 TTGATCATGTGACAACTTCAGGTGCCACTAATATGC
1 TTG---ATGTGACAACTTCAGGTGCCACTAATATTC
*
16707 TTGATGTGACAACTTCAAGTGCCACTAATATTC
1 TTGATGTGACAACTTCAGGTGCCACTAATATTC
16740 TTGATCATGTGACAACTTCAGGTGCCACTAATAT
1 TTG---ATGTGACAACTTCAGGTGCCACTAATAT
16774 ATAAGGTAGT
Statistics
Matches: 122, Mismatches: 7, Indels: 11
0.87 0.05 0.08
Matches are distributed among these distances:
32 1 0.01
33 62 0.51
36 59 0.48
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (33 bp):
TTGATGTGACAACTTCAGGTGCCACTAATATTC
Found at i:18171 original size:81 final size:81
Alignment explanation
Indices: 18080--18229 Score: 273
Period size: 81 Copynumber: 1.9 Consensus size: 81
18070 AGAGTTTCAA
* * *
18080 TGTATTTGCAAAACAAATATCATAATTAACAGCGCTTGAACCTAAAAAAATCTCTAGAAATTAAT
1 TGTATTTGCAAAACAAATAACATAATTAACAGCGCTCGAACCTAAAAAAATCTCTAGAAAGTAAT
18145 ATTTCTATTTTCAGTG
66 ATTTCTATTTTCAGTG
18161 TGTATTTGCAAAACAAATAACATAATTAACAGCGCTCGAACCTAAAAAAATCTCTAGAAAGTAAT
1 TGTATTTGCAAAACAAATAACATAATTAACAGCGCTCGAACCTAAAAAAATCTCTAGAAAGTAAT
18226 ATTT
66 ATTT
18230 TTGTTTTCGT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 66 1.00
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.31
Consensus pattern (81 bp):
TGTATTTGCAAAACAAATAACATAATTAACAGCGCTCGAACCTAAAAAAATCTCTAGAAAGTAAT
ATTTCTATTTTCAGTG
Found at i:18644 original size:5 final size:5
Alignment explanation
Indices: 18624--18662 Score: 62
Period size: 5 Copynumber: 7.8 Consensus size: 5
18614 TTTGTATAAA
18624 AAAAG -AAAG AAAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
18663 CGAAGTAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 4 0.12
5 24 0.75
6 4 0.12
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:19588 original size:42 final size:42
Alignment explanation
Indices: 19529--19609 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
19519 AGAGAGCATG
*
19529 CACCTTACAATTGACCCAAATAGTCAGATGAAGTCTAGTATA
1 CACCTTACAATTGACCCAAATACTCAGATGAAGTCTAGTATA
19571 CACCTTACAATTGACCCAAATACTCAGATGAAGTCTAGT
1 CACCTTACAATTGACCCAAATACTCAGATGAAGTCTAGT
19610 CTAGGTGAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (42 bp):
CACCTTACAATTGACCCAAATACTCAGATGAAGTCTAGTATA
Done.