Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000751.1 Corchorus capsularis cultivar CVL-1 contig00751, 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, 837
Length: 1396
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Found at i:306 original size:34 final size:34
Alignment explanation
Indices: 242--308 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
232 TGTTACAATC
* *
242 AACCAATCTATACAATTTGTAATGCATGAAAATT
1 AACCAATCTATACAATCTGTAACGCATGAAAATT
276 AACCAA-CTAGTACAATCTGTAACGTC-TGAAAAT
1 AACCAATCTA-TACAATCTGTAACG-CATGAAAAT
309 GTTAGAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 3 0.10
34 25 0.86
35 1 0.03
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.28
Consensus pattern (34 bp):
AACCAATCTATACAATCTGTAACGCATGAAAATT
Found at i:338 original size:24 final size:25
Alignment explanation
Indices: 293--340 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
283 TAGTACAATC
*
293 TGTAACGTCTGAAAATGTTAGAATT
1 TGTAACGCCTGAAAATGTTAGAATT
*
318 TGTAACGCCT-AAATTGTTAGAAT
1 TGTAACGCCTGAAAATGTTAGAAT
341 CGGCCAACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (25 bp):
TGTAACGCCTGAAAATGTTAGAATT
Found at i:388 original size:66 final size:65
Alignment explanation
Indices: 278--444 Score: 192
Period size: 66 Copynumber: 2.5 Consensus size: 65
268 TGAAAATTAA
* * * * * *
278 CCAACTAGTACAATCTGTAACG-TCTGAAAATGTTAGAATTTGTAACGCCTAAATTGTTAGAATC
1 CCAACCAGTATAATCTGTAACGCT-TGAAAAGGTTAGAATCTGTAACGCCCAAAATGTTAGAATC
342 GG
65 -G
* *
344 CCAACCAGTATAATCTGTAACGCTTGAAAGGGTTAGAATCTGTAACGCCCAAAATGTTAGTATCG
1 CCAACCAGTATAATCTGTAACGCTTGAAAAGGTTAGAATCTGTAACGCCCAAAATGTTAGAATCG
* * * *
409 ACAAGCCTGTATAATCTGTAACGCCTGAAAATGTTA
1 CCAA-CCAGTATAATCTGTAACGCTTGAAAAGGTTA
445 AAATATTAAA
Statistics
Matches: 86, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
65 4 0.05
66 81 0.94
67 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (65 bp):
CCAACCAGTATAATCTGTAACGCTTGAAAAGGTTAGAATCTGTAACGCCCAAAATGTTAGAATCG
Found at i:557 original size:42 final size:42
Alignment explanation
Indices: 505--622 Score: 191
Period size: 42 Copynumber: 2.8 Consensus size: 42
495 CAGCCAACCT
* * * **
505 ATACAGTCTGTAACACCTAAAAATGTTAGAATTAACCAACTA
1 ATACAATCTGTAACATCTGAAGTTGTTAGAATTAACCAACTA
547 ATACAATCTGTAACATCTGAAGTTGTTAGAATTAACCAACTA
1 ATACAATCTGTAACATCTGAAGTTGTTAGAATTAACCAACTA
589 ATACAATCTGTAACATCTGAAGTTGTTAGAATTA
1 ATACAATCTGTAACATCTGAAGTTGTTAGAATTA
623 GCAATCAAAA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.31
Consensus pattern (42 bp):
ATACAATCTGTAACATCTGAAGTTGTTAGAATTAACCAACTA
Found at i:651 original size:41 final size:42
Alignment explanation
Indices: 528--651 Score: 155
Period size: 42 Copynumber: 3.0 Consensus size: 42
518 CACCTAAAAA
* *
528 TGTTAGAATTAACCAACTAATACAATCTGTAACATCTGAAGT
1 TGTTAGAATTAACCAACTAAAACAATCTATAACATCTGAAGT
* *
570 TGTTAGAATTAACCAACTAATACAATCTGTAACATCTGAAGT
1 TGTTAGAATTAACCAACTAAAACAATCTATAACATCTGAAGT
* *
612 TGTTAGAATT-AGCAA-TCAAAACAATTTATAAC-TCATGAAG
1 TGTTAGAATTAACCAACT-AAAACAATCTATAACATC-TGAAG
652 ATCAACCAAC
Statistics
Matches: 76, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
40 3 0.04
41 21 0.28
42 52 0.68
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (42 bp):
TGTTAGAATTAACCAACTAAAACAATCTATAACATCTGAAGT
Found at i:702 original size:83 final size:84
Alignment explanation
Indices: 603--771 Score: 250
Period size: 84 Copynumber: 2.0 Consensus size: 84
593 AATCTGTAAC
* * * * *
603 ATCTGAAGTTGTTAGAATTAGC-AATCAAAACAATTTATAACTCATGAAGATCAACCAACTAGTA
1 ATCTGAAATTGATAGAATTAGCTAACCAAAACAATTTATAACGCATGAAAATCAACCAACTAGTA
* *
667 CCATCCATAATGCATGAAA
66 CAATCCATAATGCACGAAA
*
686 ATCTGAAATTGATAGAATTAGCTAACCAAAACAATTTATAACGCATGAAAATGAACCAACTAGTA
1 ATCTGAAATTGATAGAATTAGCTAACCAAAACAATTTATAACGCATGAAAATCAACCAACTAGTA
*
751 CAATCTATAATGCACGAAA
66 CAATCCATAATGCACGAAA
770 AT
1 AT
772 GAACTAACCA
Statistics
Matches: 76, Mismatches: 9, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
83 20 0.26
84 56 0.74
ACGTcount: A:0.46, C:0.17, G:0.12, T:0.25
Consensus pattern (84 bp):
ATCTGAAATTGATAGAATTAGCTAACCAAAACAATTTATAACGCATGAAAATCAACCAACTAGTA
CAATCCATAATGCACGAAA
Found at i:796 original size:34 final size:34
Alignment explanation
Indices: 716--797 Score: 110
Period size: 34 Copynumber: 2.4 Consensus size: 34
706 GCTAACCAAA
* * * *
716 ACAATTTATAACGCATGAAAATGAACCAACTAGT
1 ACAATCTATAATGCACGAAAATGAACCAACCAGT
*
750 ACAATCTATAATGCACGAAAATGAACTAACCAGT
1 ACAATCTATAATGCACGAAAATGAACCAACCAGT
*
784 ACAATCTCTAATGC
1 ACAATCTATAATGC
798 TTATACTACT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.45, C:0.21, G:0.11, T:0.23
Consensus pattern (34 bp):
ACAATCTATAATGCACGAAAATGAACCAACCAGT
Done.