Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003895.1 Corchorus capsularis cultivar CVL-1 contig03903, 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, 646
Length: 1077
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:136 original size:43 final size:43
Alignment explanation
Indices: 41--155 Score: 128
Period size: 43 Copynumber: 2.7 Consensus size: 43
31 ATCTCATGGT
* * * *
41 TCAAAATTTAAAACCTGCATTACA-CGGTTC-ATTCTTCAAAAG
1 TCAAAATTCAAAACTTGCATTTCAGC-ATTCTATTCTTCAAAAG
83 TCAAAATTCAAAACTTGCATTTCAGCATTCTATTCTTCGAAAA-
1 TCAAAATTCAAAACTTGCATTTCAGCATTCTATTCTTC-AAAAG
* * *
126 TCAAAGTTCAAAATTTGCATTTCATCATTC
1 TCAAAATTCAAAACTTGCATTTCAGCATTC
156 AAAAATCAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
42 24 0.38
43 35 0.56
44 4 0.06
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.35
Consensus pattern (43 bp):
TCAAAATTCAAAACTTGCATTTCAGCATTCTATTCTTCAAAAG
Found at i:161 original size:35 final size:34
Alignment explanation
Indices: 116--342 Score: 127
Period size: 35 Copynumber: 6.4 Consensus size: 34
106 AGCATTCTAT
*
116 TCTTCGAAAATCAAAGTTCAAAATTTGCATTTCA
1 TCTTCAAAAATCAAAGTTCAAAATTTGCATTTCA
** *
150 TCATTCAAAAATCAAAGTTCAAAATCAGCATCTCA
1 TC-TTCAAAAATCAAAGTTCAAAATTTGCATTTCA
* * * *** * *
185 TGGTTCAAAATTCAAA-ATCTGCATTT-CACGGTTCGT
1 T-CTTCAAAAATCAAAGTTCAAAATTTGCA--TTTC-A
* * *
221 TCTTCAAAAGTCAAAATTCAAAACTTGCATTTCAACA
1 TCTTCAAAAATCAAAGTTCAAAATTTGCATTT---CA
* *
258 TTCCTTTCGAAAATCAAAATTCAAAATTTGCATTTCA
1 -T-C-TTCAAAAATCAAAGTTCAAAATTTGCATTTCA
* * * *
295 T-TTCAAAATTCAATGTTCAAAATCTGCATCTCA
1 TCTTCAAAAATCAAAGTTCAAAATTTGCATTTCA
* *
328 TGTTCAAAACTCAAA
1 TCTTCAAAAATCAAA
343 ATCCAGCATC
Statistics
Matches: 144, Mismatches: 35, Indels: 28
0.70 0.17 0.14
Matches are distributed among these distances:
33 29 0.20
34 17 0.12
35 57 0.40
36 7 0.05
37 4 0.03
38 2 0.01
39 1 0.01
40 27 0.19
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (34 bp):
TCTTCAAAAATCAAAGTTCAAAATTTGCATTTCA
Found at i:192 original size:28 final size:28
Alignment explanation
Indices: 161--218 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
151 CATTCAAAAA
* *
161 TCAAAGTTCAAAATCAGCATCTCATGGT
1 TCAAAATTCAAAATCAGCATCTCACGGT
* *
189 TCAAAATTCAAAATCTGCATTTCACGGT
1 TCAAAATTCAAAATCAGCATCTCACGGT
217 TC
1 TC
219 GTTCTTCAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.31
Consensus pattern (28 bp):
TCAAAATTCAAAATCAGCATCTCACGGT
Found at i:289 original size:40 final size:43
Alignment explanation
Indices: 189--294 Score: 132
Period size: 40 Copynumber: 2.6 Consensus size: 43
179 ATCTCATGGT
* * *
189 TCAAAATTCAAAATCTGCATTTC-ACGGTTCGTTCTTCAAAAG
1 TCAAAATTCAAAATTTGCATTTCAACGATTCGCTCTTCAAAAG
*
231 TCAAAATTCAAAACTTGCATTTCAAC-ATTC-CT-TTCGAAAA-
1 TCAAAATTCAAAATTTGCATTTCAACGATTCGCTCTTC-AAAAG
271 TCAAAATTCAAAATTTGCATTTCA
1 TCAAAATTCAAAATTTGCATTTCA
295 TTTCAAAATT
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
40 26 0.46
41 5 0.09
42 24 0.42
43 2 0.04
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.34
Consensus pattern (43 bp):
TCAAAATTCAAAATTTGCATTTCAACGATTCGCTCTTCAAAAG
Found at i:314 original size:33 final size:34
Alignment explanation
Indices: 277--341 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
267 AAAATCAAAA
* * *
277 TTCAAAATTTGCATTTCAT-TTCAAAATTCAATG
1 TTCAAAATCTGCATCTCATGTTCAAAACTCAATG
310 TTCAAAATCTGCATCTCATGTTCAAAACTCAA
1 TTCAAAATCTGCATCTCATGTTCAAAACTCAA
342 AATCCAGCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 17 0.61
34 11 0.39
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (34 bp):
TTCAAAATCTGCATCTCATGTTCAAAACTCAATG
Done.