Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010741.1 Corchorus olitorius cultivar O-4 contig10773, 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: 52196
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:633 original size:11 final size:11
Alignment explanation
Indices: 610--653 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
600 TTTGGCATCG
*
610 TTTTTGTTT-T
1 TTTTTTTTTGT
620 TTTTTTTTTGT
1 TTTTTTTTTGT
*
631 TTTTTTTTCGT
1 TTTTTTTTTGT
*
642 TTTGTTTTTGT
1 TTTTTTTTTGT
653 T
1 T
654 GCGCTGTCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
10 8 0.28
11 21 0.72
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.86
Consensus pattern (11 bp):
TTTTTTTTTGT
Found at i:635 original size:16 final size:16
Alignment explanation
Indices: 611--650 Score: 66
Period size: 14 Copynumber: 2.6 Consensus size: 16
601 TTGGCATCGT
611 TTTTGTTTTTTTTT--
1 TTTTGTTTTTTTTTCG
625 TTTTGTTTTTTTTTCG
1 TTTTGTTTTTTTTTCG
641 TTTTGTTTTT
1 TTTTGTTTTT
651 GTTGCGCTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 14 0.58
16 10 0.42
ACGTcount: A:0.00, C:0.03, G:0.10, T:0.88
Consensus pattern (16 bp):
TTTTGTTTTTTTTTCG
Found at i:13575 original size:15 final size:15
Alignment explanation
Indices: 13552--13581 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13542 CACGTAAGAT
13552 TAAAAAATAAATAAA
1 TAAAAAATAAATAAA
*
13567 TAAATAATAAATAAA
1 TAAAAAATAAATAAA
13582 ATATATAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
TAAAAAATAAATAAA
Found at i:20647 original size:7 final size:7
Alignment explanation
Indices: 20635--20663 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
20625 TAAAATTGGA
20635 ACTTCTC
1 ACTTCTC
20642 ACTTCTC
1 ACTTCTC
20649 ACTTCTC
1 ACTTCTC
20656 ACTTCTC
1 ACTTCTC
20663 A
1 A
20664 TAGGAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.17, C:0.41, G:0.00, T:0.41
Consensus pattern (7 bp):
ACTTCTC
Found at i:35657 original size:11 final size:11
Alignment explanation
Indices: 35637--35669 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
35627 TATATCTGAG
35637 TTTTCTTTTTCT
1 TTTTC-TTTTCT
35649 TTTTCTTTTCT
1 TTTTCTTTTCT
35660 TTTT-TTTTCT
1 TTTTCTTTTCT
35670 CCCTTCCCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 6 0.29
11 10 0.48
12 5 0.24
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTCTTTTCT
Found at i:36861 original size:28 final size:28
Alignment explanation
Indices: 36829--36884 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
36819 ATCCTTATAC
36829 TATTATTACTTTTTCTTTTTTCTCAACA
1 TATTATTACTTTTTCTTTTTTCTCAACA
36857 TATTATTACTTTTTCTTTTTTCTCAACA
1 TATTATTACTTTTTCTTTTTTCTCAACA
36885 AAAGTTTAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.21, C:0.18, G:0.00, T:0.61
Consensus pattern (28 bp):
TATTATTACTTTTTCTTTTTTCTCAACA
Found at i:38038 original size:2 final size:2
Alignment explanation
Indices: 38031--38063 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
38021 TTACATAGTG
38031 TA TA 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 TA TA T
38064 TTGTGTCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39548 original size:2 final size:2
Alignment explanation
Indices: 39503--39528 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39493 CTATAAAAAA
39503 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
39529 GCAGGAGCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43612 original size:2 final size:2
Alignment explanation
Indices: 43605--43635 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
43595 TAATAACTAC
43605 TA 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 TA T
43636 CAACAACCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44243 original size:30 final size:30
Alignment explanation
Indices: 44209--44277 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
44199 CTTCACTATC
44209 TTCTACCACCTCTTCCTCGTCCTCTCAAAT
1 TTCTACCACCTCTTCCTCGTCCTCTCAAAT
*
44239 TTCTACCACCTCTTCCTTGTCCTCTCAAAT
1 TTCTACCACCTCTTCCTCGTCCTCTCAAAT
*
44269 TTCTTCCAC
1 TTCTACCAC
44278 ATCAACCATG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.16, C:0.42, G:0.03, T:0.39
Consensus pattern (30 bp):
TTCTACCACCTCTTCCTCGTCCTCTCAAAT
Found at i:45313 original size:22 final size:21
Alignment explanation
Indices: 45288--45341 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
45278 GAAGTTCGTG
45288 TTTGAAGACTTATTGAAGATAA
1 TTTGAAGA-TTATTGAAGATAA
*
45310 TTTGAAGA-T-TTGAAGATCA
1 TTTGAAGATTATTGAAGATAA
45329 -TTGAAGAATTATT
1 TTTGAAG-ATTATT
45342 TCAAGAAGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39
Consensus pattern (21 bp):
TTTGAAGATTATTGAAGATAA
Found at i:49267 original size:23 final size:23
Alignment explanation
Indices: 49241--49286 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
49231 GAACTTTAGT
*
49241 GAGTTTCTATTTTGATATAGCTA
1 GAGTTTCTACTTTGATATAGCTA
49264 GAGTTTCTACTTTGATATAGCTA
1 GAGTTTCTACTTTGATATAGCTA
49287 TAAAAAGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.46
Consensus pattern (23 bp):
GAGTTTCTACTTTGATATAGCTA
Done.