Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014315.1 Corchorus capsularis cultivar CVL-1 contig14336, 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: 39059
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3891 original size:10 final size:10
Alignment explanation
Indices: 3876--3901 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3866 GAGGACTCTA
3876 GAATTTTCTG
1 GAATTTTCTG
3886 GAATTTTCTG
1 GAATTTTCTG
3896 GAATTT
1 GAATTT
3902 GGCAGCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.19, T:0.50
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:13726 original size:36 final size:36
Alignment explanation
Indices: 13686--13758 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
13676 TCCTTAAGGA
13686 ATAGTTTTGAACATTAAATATATATAATTAATTAGG
1 ATAGTTTTGAACATTAAATATATATAATTAATTAGG
13722 ATAGTTTTGAACATTAAATATATATAATTAATTAGG
1 ATAGTTTTGAACATTAAATATATATAATTAATTAGG
13758 A
1 A
13759 GATATGGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.45, C:0.03, G:0.11, T:0.41
Consensus pattern (36 bp):
ATAGTTTTGAACATTAAATATATATAATTAATTAGG
Found at i:14304 original size:11 final size:11
Alignment explanation
Indices: 14261--14298 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
14251 TTCCTATATA
*
14261 AAATAAATTAT
1 AAATTAATTAT
14272 CAAA-TAATTAT
1 -AAATTAATTAT
14283 AAATTAATTAT
1 AAATTAATTAT
14294 AAATT
1 AAATT
14299 TGTTATGTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:14550 original size:16 final size:17
Alignment explanation
Indices: 14525--14559 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
14515 TCTTCTCCAT
14525 ATTCTATTGTC-TTTCC
1 ATTCTATTGTCTTTTCC
*
14541 ATTCTCTTGTCTTTTCC
1 ATTCTATTGTCTTTTCC
14558 AT
1 AT
14560 GCTTCAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.11, C:0.26, G:0.06, T:0.57
Consensus pattern (17 bp):
ATTCTATTGTCTTTTCC
Found at i:14691 original size:41 final size:42
Alignment explanation
Indices: 14619--14702 Score: 152
Period size: 41 Copynumber: 2.0 Consensus size: 42
14609 ACAAAATATC
*
14619 ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
1 ATTTATTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
14661 ATTTATTAACTGAA-TTTTCTTAAAAGAATTTATAAAATAAA
1 ATTTATTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
14702 A
1 A
14703 CAGCCGCACA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
41 28 0.68
42 13 0.32
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.42
Consensus pattern (42 bp):
ATTTATTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
Found at i:16318 original size:180 final size:176
Alignment explanation
Indices: 15962--16319 Score: 592
Period size: 180 Copynumber: 2.0 Consensus size: 176
15952 TCCGTAAACA
*
15962 AATCATTTTTTGTTGGATTATTTATTAAATGATCCTCATACTTTTATAATTTATGCTATTTAATC
1 AATCATTTTTTGTTGGATTATTTATTAAATGATCCTCATACTTTTATAATTTATACTATTTAATC
* *
16027 CTTACAAATATATTCTGGACGATTGAATGTTTCGGCTTTAATTATTTTTTTTTTCTATTTAACCT
66 CTTACAAATATAGTCTGGACGATTGAATGTTTCGGCTTTAATTATTTTTTTTTTCTATTTAACCG
*
16092 ATCAAGGTGATTCAGGTGTCTATTTAAAGGTAATTCCATGGTCTAC
131 ATCAAGGTGATTCAAGTGTCTATTTAAAGGTAATTCCATGGTCTAC
16138 AATCATTTTTTTGTTGGATTATTTATTAAATGATCCTCATACTTTTATAATTTATACTATTTAAT
1 AATCA-TTTTTTGTTGGATTATTTATTAAATGATCCTCATACTTTTATAATTTATACTATTTAAT
* * *
16203 CACTTACAATTATGGGT-TGGACGATTGAATGTTTCGGCTTTAATTCTTTTATTTTTTTCTATTT
65 C-CTTACAAATAT-AGTCTGGACGATTGAATGTTTCGGCTTTAATT-ATTT-TTTTTTTCTATTT
*
16267 GACCGATCAAGGTGATTCAAGTGTCTATTTAAAGGTAATTCCATGGTCTAC
126 AACCGATCAAGGTGATTCAAGTGTCTATTTAAAGGTAATTCCATGGTCTAC
16318 AA
1 AA
16320 CTTTCATGAA
Statistics
Matches: 169, Mismatches: 8, Indels: 6
0.92 0.04 0.03
Matches are distributed among these distances:
176 5 0.03
177 59 0.35
178 38 0.22
179 4 0.02
180 63 0.37
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (176 bp):
AATCATTTTTTGTTGGATTATTTATTAAATGATCCTCATACTTTTATAATTTATACTATTTAATC
CTTACAAATATAGTCTGGACGATTGAATGTTTCGGCTTTAATTATTTTTTTTTTCTATTTAACCG
ATCAAGGTGATTCAAGTGTCTATTTAAAGGTAATTCCATGGTCTAC
Found at i:23757 original size:2 final size:2
Alignment explanation
Indices: 23750--23781 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
23740 CAGTGAAACA
23750 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23782 GTTATAGCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33899 original size:11 final size:12
Alignment explanation
Indices: 33881--33917 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
33871 ATAGATATAT
33881 AATATAATAATA
1 AATATAATAATA
33893 AAT-TAATAA-A
1 AATATAATAATA
33903 AATATAATAAATA
1 AATATAAT-AATA
33916 AA
1 AA
33918 ATGGAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
10 4 0.18
11 10 0.45
12 5 0.23
13 3 0.14
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AATATAATAATA
Found at i:34334 original size:2 final size:2
Alignment explanation
Indices: 34327--34358 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
34317 CCCTTTCAAG
34327 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34359 ATCAATGCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:37742 original size:2 final size:2
Alignment explanation
Indices: 37735--37763 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
37725 TGAGCTCAAT
37735 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
37764 TAAGGATTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.