Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010011.1 Corchorus capsularis cultivar CVL-1 contig10032, 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: 23552
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:5698 original size:18 final size:18
Alignment explanation
Indices: 5675--5709 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5665 TTACTTAACA
5675 AAATTTTTATCCCCACAC
1 AAATTTTTATCCCCACAC
*
5693 AAATTTTTGTCCCCACA
1 AAATTTTTATCCCCACA
5710 GCGAAGCGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.31, G:0.03, T:0.34
Consensus pattern (18 bp):
AAATTTTTATCCCCACAC
Found at i:8657 original size:2 final size:2
Alignment explanation
Indices: 8650--8677 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
8640 TTCAGGTATG
8650 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
8678 ATCAAATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11360 original size:2 final size:2
Alignment explanation
Indices: 11344--11398 Score: 59
Period size: 2 Copynumber: 30.0 Consensus size: 2
11334 CCCGTATTAG
11344 TA TA TA -A TA TA -A TA TA TA T- TA TA T- TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11381 GTA TA -A TA TA TA TA TA TA
1 -TA TA TA TA TA TA TA TA TA
11399 CCATAATACA
Statistics
Matches: 46, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
1 6 0.13
2 38 0.83
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:11502 original size:16 final size:16
Alignment explanation
Indices: 11471--11500 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
11461 ACAATATATA
11471 TATATATTATAAAAAT
1 TATATATTATAAAAAT
11487 TATAT-TTATAAAAA
1 TATATATTATAAAAA
11501 ATATGGCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TATATATTATAAAAAT
Found at i:19721 original size:16 final size:15
Alignment explanation
Indices: 19673--19714 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
19663 GAAAGGTGGT
19673 ATATTTAA--TTTTA
1 ATATTTAATTTTTTA
*
19686 CTATTTAATTTTTTA
1 ATATTTAATTTTTTA
19701 ATATTTAATTTTTT
1 ATATTTAATTTTTT
19715 GTGTATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 7 0.28
15 18 0.72
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (15 bp):
ATATTTAATTTTTTA
Found at i:21364 original size:109 final size:109
Alignment explanation
Indices: 21168--21463 Score: 459
Period size: 109 Copynumber: 2.7 Consensus size: 109
21158 ACTATTATAG
* *
21168 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
21233 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
21282 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
*
21347 TTACCAAAAAATTTGGATATATTAAAATTTTTTCTAATATACAA
66 TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
* **
21391 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATATTTTATATAATTTTTTTTA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTT-TATAA-TTACTTTA
21455 TTTTTACCA
63 TTTTTACCA
21464 TTTTAATTTA
Statistics
Matches: 173, Mismatches: 6, Indels: 9
0.92 0.03 0.05
Matches are distributed among these distances:
108 1 0.01
109 126 0.73
110 8 0.05
111 17 0.10
114 21 0.12
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Found at i:23194 original size:23 final size:21
Alignment explanation
Indices: 23139--23198 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
23129 TGAATATTTT
*
23139 TATGAAATTTTGATAACTACC
1 TATGAAATTTTGATAACCACC
*
23160 TATTAAATTTTGATAACCCACAC
1 TATGAAATTTTGATAA-CCAC-C
*
23183 TATGAAAATTTGATAA
1 TATGAAATTTTGATAA
23199 TTTTCCTATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 15 0.45
22 3 0.09
23 15 0.45
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (21 bp):
TATGAAATTTTGATAACCACC
Found at i:23528 original size:2 final size:2
Alignment explanation
Indices: 23523--23552 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
23513 ATATATATAT
23523 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.