Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008406.1 Corchorus capsularis cultivar CVL-1 contig08427, 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: 54564
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:5897 original size:23 final size:23
Alignment explanation
Indices: 5848--5897 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
5838 ATAATTTGTT
* *
5848 AAAAAGAATAAAAAAATGGAAAG
1 AAAAAGAATAAAAAAAAGGAAAC
*
5871 AAAATGAATAAAAAAAAGCG-AAC
1 AAAAAGAATAAAAAAAAG-GAAAC
5894 AAAA
1 AAAA
5898 CGCTTTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.74, C:0.04, G:0.14, T:0.08
Consensus pattern (23 bp):
AAAAAGAATAAAAAAAAGGAAAC
Found at i:18168 original size:19 final size:18
Alignment explanation
Indices: 18144--18180 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
18134 GAAGTTCGTG
18144 TTTGAAGATAATTTGAAGA
1 TTTGAAGATAA-TTGAAGA
*
18163 TTTGAAGATCATTGAAGA
1 TTTGAAGATAATTGAAGA
18181 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.35
Consensus pattern (18 bp):
TTTGAAGATAATTGAAGA
Found at i:32052 original size:54 final size:54
Alignment explanation
Indices: 31962--32086 Score: 189
Period size: 54 Copynumber: 2.3 Consensus size: 54
31952 TTTTGTGTCC
* * *
31962 TAATTATAAATTGAGTTATATATTAGATGATTTTAGGAACTTAATTTCTTCTTAT
1 TAATTTTAAATT-ATTTATATATTAGATGATCTTAGGAACTTAATTTCTTCTTAT
*
32017 TAATTTTAAATTATTTATATATTATATCG-TCTTAGGAACTTAATTTCTTCTTAT
1 TAATTTTAAATTATTTATATATTAGAT-GATCTTAGGAACTTAATTTCTTCTTAT
32071 TAATTTTAAATTATTT
1 TAATTTTAAATTATTT
32087 TGTGTCTTAA
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
54 53 0.82
55 12 0.18
ACGTcount: A:0.34, C:0.06, G:0.07, T:0.53
Consensus pattern (54 bp):
TAATTTTAAATTATTTATATATTAGATGATCTTAGGAACTTAATTTCTTCTTAT
Found at i:36477 original size:23 final size:22
Alignment explanation
Indices: 36443--36486 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
36433 TTTTTCTGCT
* **
36443 TTTTATTCTCAAGTTCATGTTC
1 TTTTATTATCAAACTCATGTTC
36465 TTTTAGTTATCAAACTCATGTT
1 TTTTA-TTATCAAACTCATGTT
36487 TGGAGCCTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.23, C:0.16, G:0.09, T:0.52
Consensus pattern (22 bp):
TTTTATTATCAAACTCATGTTC
Found at i:37877 original size:40 final size:41
Alignment explanation
Indices: 37772--37879 Score: 123
Period size: 41 Copynumber: 2.7 Consensus size: 41
37762 AAAATGCCAT
* * *
37772 AAAACTAAGCTAAACCCTAAGAGAGAGGATAAACACCTCCT
1 AAAACTAAGCTAAACCCTAAGAGAGATGATAAAAACCTCCC
*
37813 AAAACTAAGCTAAAACC-AAGGAGAGATGA-AACAAACC-CCC
1 AAAACTAAGCTAAACCCTAA-GAGAGATGATAA-AAACCTCCC
* *
37853 AAAACCAAGTTAAACCCTAAGAGAGAT
1 AAAACTAAGCTAAACCCTAAGAGAGAT
37880 AACCATGAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
40 27 0.47
41 30 0.53
ACGTcount: A:0.50, C:0.23, G:0.15, T:0.12
Consensus pattern (41 bp):
AAAACTAAGCTAAACCCTAAGAGAGATGATAAAAACCTCCC
Found at i:40408 original size:16 final size:16
Alignment explanation
Indices: 40389--40425 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
40379 AAGTTCAAAT
*
40389 CCGAAAAAATCAGAAC
1 CCGAAAAAACCAGAAC
*
40405 CCGAAAAAACCCGAAC
1 CCGAAAAAACCAGAAC
40421 CCGAA
1 CCGAA
40426 TCCGAAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.32, G:0.14, T:0.03
Consensus pattern (16 bp):
CCGAAAAAACCAGAAC
Found at i:41416 original size:31 final size:31
Alignment explanation
Indices: 41378--41436 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
41368 TTTGTAAAAC
* * *
41378 TTTTGAAATACCTATTATGCCCTTATTTAAT
1 TTTTGAAACACCAATTATACCCTTATTTAAT
*
41409 TTTTGAAACACCAATTATATCCTTATTT
1 TTTTGAAACACCAATTATACCCTTATTT
41437 GTCTAACATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.31, C:0.17, G:0.05, T:0.47
Consensus pattern (31 bp):
TTTTGAAACACCAATTATACCCTTATTTAAT
Found at i:49743 original size:21 final size:21
Alignment explanation
Indices: 49700--49744 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
49690 AATGGAGATC
* * *
49700 ATGTCTCGGATAAACATGGAG
1 ATGTCTCGGACAAACAAGAAG
*
49721 ATGTCTCGGACAATCAAGAAG
1 ATGTCTCGGACAAACAAGAAG
49742 ATG
1 ATG
49745 CCAAGGTTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.16, G:0.27, T:0.22
Consensus pattern (21 bp):
ATGTCTCGGACAAACAAGAAG
Found at i:52994 original size:10 final size:9
Alignment explanation
Indices: 52977--53004 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
52967 GATTAATTAA
52977 TATTTTTTT
1 TATTTTTTT
52986 TATTTTTTT
1 TATTTTTTT
52995 TATTTTTTT
1 TATTTTTTT
53004 T
1 T
53005 GCAAGAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (9 bp):
TATTTTTTT
Found at i:54460 original size:36 final size:36
Alignment explanation
Indices: 54418--54531 Score: 160
Period size: 36 Copynumber: 3.2 Consensus size: 36
54408 CTCTTCTTAG
* *
54418 ATTAAG-CTCTTTATTGACTCCACTTAATTACCCTAA
1 ATTAAGCCT-TTTATTGACTCTACTTAATTACCCTGA
54454 ATTAAGCCTTTTATTGACGT-TACTTAATTACCCTGA
1 ATTAAGCCTTTTATTGAC-TCTACTTAATTACCCTGA
* *
54490 ATTAAGCCTTTTATTGACGCTACTTAATTACCCCGA
1 ATTAAGCCTTTTATTGACTCTACTTAATTACCCTGA
54526 ATTAAG
1 ATTAAG
54532 TCCCTAACTT
Statistics
Matches: 71, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
36 68 0.96
37 3 0.04
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.39
Consensus pattern (36 bp):
ATTAAGCCTTTTATTGACTCTACTTAATTACCCTGA
Done.