Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000089.1 Corchorus capsularis cultivar CVL-1 contig00089, 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, 771
Length: 1286
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:236 original size:68 final size:69
Alignment explanation
Indices: 1--275 Score: 353
Period size: 69 Copynumber: 4.0 Consensus size: 69
* *
1 CAAACTTGTTTCCACACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCAGCGGCTTTTCCAC
1 CAAACTCGTTTCCACACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCAGAGGCTTTTCCAC
66 AAGC
66 AAGC
* * ** * *
70 CAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATTTAGGGGCTTTCCCA
1 CAAACTCGTTTCCACACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCA-GCAGAGGCTTTTCCA
135 CAAGC
65 CAAGC
* * *
140 CAAACTCGTTTCCACACGAGTCAATT-TAGCCTTGGTTCCATCCAAGCAGCAAAGGCTTTTCCAC
1 CAAACTCGTTTCCACACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCAGAGGCTTTTCCAC
*
204 TAGC
66 AAGC
* * * * *
208 CAAACTCGTTTCCATATGAGTTAGTT-TAGCCTTGGTTCCATCCAAGCAG--G-GGCTTTTCCAT
1 CAAACTCGTTTCCACACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCAGAGGCTTTTCCAC
269 AAGC
66 AAGC
273 CAA
1 CAA
276 GTTCATTTCC
Statistics
Matches: 181, Mismatches: 24, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
65 16 0.09
68 59 0.33
69 66 0.36
70 40 0.22
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (69 bp):
CAAACTCGTTTCCACACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCAGAGGCTTTTCCAC
AAGC
Found at i:495 original size:12 final size:11
Alignment explanation
Indices: 479--548 Score: 72
Period size: 10 Copynumber: 6.2 Consensus size: 11
469 AAAATAATAT
479 AAAAAAATGAATG
1 AAAAAAA-GAA-G
492 AAAAAAAGAAG
1 AAAAAAAGAAG
*
503 AAAAAAAAGGAAA
1 -AAAAAAA-GAAG
516 AAAAAAAGAA-
1 AAAAAAAGAAG
526 AAAAAAAGAA-
1 AAAAAAAGAAG
*
536 AAAGAAAGAAG
1 AAAAAAAGAAG
547 AA
1 AA
549 GCCAAAAAGG
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
10 19 0.37
11 6 0.12
12 17 0.33
13 10 0.19
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (11 bp):
AAAAAAAGAAG
Found at i:506 original size:10 final size:10
Alignment explanation
Indices: 491--545 Score: 74
Period size: 10 Copynumber: 5.3 Consensus size: 10
481 AAAAATGAAT
491 GAAAAAAAGAA
1 GAAAAAAA-AA
*
502 GAAAAAAAAG
1 GAAAAAAAAA
512 GAAAAAAAAAA
1 G-AAAAAAAAA
523 GAAAAAAAAA
1 GAAAAAAAAA
*
533 GAAAAAGAAA
1 GAAAAAAAAA
543 GAA
1 GAA
546 GAAGCCAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
10 23 0.57
11 17 0.43
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:510 original size:13 final size:12
Alignment explanation
Indices: 479--548 Score: 71
Period size: 12 Copynumber: 6.2 Consensus size: 12
469 AAAATAATAT
*
479 AAAAAAATGAATG
1 AAAAAAAAGAA-G
492 -AAAAAAAGAAG
1 AAAAAAAAGAAG
503 AAAAAAAAG--G
1 AAAAAAAAGAAG
513 AAAAAAAA-AAG
1 AAAAAAAAGAAG
524 -AAAAAAA-AAG
1 AAAAAAAAGAAG
534 AAAAAGAAAGAAG
1 AAAAA-AAAGAAG
547 AA
1 AA
549 GCCAAAAAGG
Statistics
Matches: 50, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
10 19 0.38
11 6 0.12
12 20 0.40
13 5 0.10
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (12 bp):
AAAAAAAAGAAG
Found at i:515 original size:21 final size:21
Alignment explanation
Indices: 491--548 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
481 AAAAATGAAT
491 GAAAAAAAGAAGAAAAAAAAG
1 GAAAAAAAGAAGAAAAAAAAG
*
512 GAAAAAAAAAAGAAAAAAAAAG
1 GAAAAAAAGAAG-AAAAAAAAG
*
534 AAAAAGAAAGAAGAA
1 GAAAA-AAAGAAGAA
549 GCCAAAAAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.34
22 15 0.47
23 6 0.19
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (21 bp):
GAAAAAAAGAAGAAAAAAAAG
Found at i:772 original size:27 final size:27
Alignment explanation
Indices: 740--814 Score: 96
Period size: 28 Copynumber: 2.7 Consensus size: 27
730 AGGGTCACAT
740 AGGGGCATTTTGGTCATTTTCACATTC
1 AGGGGCATTTTGGTCATTTTCACATTC
** *
767 AGGGGCATTTTGGTCATTTTTTGCATTT
1 AGGGGCATTTTGGTCA-TTTTCACATTC
* *
795 AAGGGTATTTTGGTCATTTT
1 AGGGGCATTTTGGTCATTTT
815 AAGTTCACTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
27 20 0.48
28 22 0.52
ACGTcount: A:0.17, C:0.12, G:0.24, T:0.47
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTTCACATTC
Found at i:1267 original size:23 final size:23
Alignment explanation
Indices: 1237--1281 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
1227 ATTTCATTAA
1237 GAGTTAATCTTGGACTTGTCTCT
1 GAGTTAATCTTGGACTTGTCTCT
1260 GAGTTAATCTTGGACTTGTCTC
1 GAGTTAATCTTGGACTTGTCTC
1282 CTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42
Consensus pattern (23 bp):
GAGTTAATCTTGGACTTGTCTCT
Done.