Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014014.1 Corchorus olitorius cultivar O-4 contig14047, 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: 33967
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Found at i:143 original size:26 final size:26
Alignment explanation
Indices: 105--171 Score: 93
Period size: 26 Copynumber: 2.5 Consensus size: 26
95 GTGTCTTTGA
105 AAAAAAAAGAGTTTTCGT-TTTTGCGAT-
1 AAAAAAAA-AGTTTT-GTGTTTTGCG-TC
132 AAAAAAAAAGTTTTGTGTTTTGCGTC
1 AAAAAAAAAGTTTTGTGTTTTGCGTC
158 AAAAAAAAAGTTTT
1 AAAAAAAAAGTTTT
172 TGCATCATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
25 3 0.08
26 27 0.71
27 8 0.21
ACGTcount: A:0.42, C:0.06, G:0.16, T:0.36
Consensus pattern (26 bp):
AAAAAAAAAGTTTTGTGTTTTGCGTC
Found at i:3344 original size:21 final size:21
Alignment explanation
Indices: 3320--3368 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
3310 CCATTCACCA
*
3320 TGCCATCACTGGTTAAGCCCG
1 TGCCATCACCGGTTAAGCCCG
* * *
3341 TGCCACCACCGGTTACGCCTG
1 TGCCATCACCGGTTAAGCCCG
3362 TGCCATC
1 TGCCATC
3369 GCCATTCCAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.16, C:0.39, G:0.22, T:0.22
Consensus pattern (21 bp):
TGCCATCACCGGTTAAGCCCG
Found at i:4721 original size:24 final size:28
Alignment explanation
Indices: 4684--4743 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 28
4674 ACGACCGATC
4684 AAGTATATAGTATATATG-T-TA-AAGAA
1 AAGTATA-AGTATATATGATGTATAAGAA
4710 AAGTATAA-TATATATGATGTATAAGAA
1 AAGTATAAGTATATATGATGTATAAGAA
4737 AA-TATAA
1 AAGTATAA
4744 AATAAATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.26
25 2 0.06
26 14 0.45
27 7 0.23
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.33
Consensus pattern (28 bp):
AAGTATAAGTATATATGATGTATAAGAA
Found at i:4723 original size:26 final size:26
Alignment explanation
Indices: 4684--4752 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
4674 ACGACCGATC
4684 AAGTAT-ATAGTATATATGT-TAAAGAA
1 AAGTATAATA-TATATATGTAT-AAGAA
4710 AAGTATAATATATATGATGTATAAGAA
1 AAGTATAATATATAT-ATGTATAAGAA
* *
4737 AA-TATAAAATAAATAT
1 AAGTATAATATATATAT
4753 ATTTAGTGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
25 2 0.05
26 21 0.55
27 14 0.37
28 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (26 bp):
AAGTATAATATATATATGTATAAGAA
Found at i:10291 original size:31 final size:31
Alignment explanation
Indices: 10247--10387 Score: 174
Period size: 31 Copynumber: 4.5 Consensus size: 31
10237 ATGGTGTCTG
*
10247 ACGTGGCATGCCACGTGTACCAAAAAGCGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
* *
10278 ATGTGGCACGCCACGTGTACCAAAAAGTGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
** * * *
10309 ACGTATCACGCCATGTGTACCAAAAAGTGAT
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
* * **
10340 ATGTGGCATGCCAAGTGTTTCAAAAAGTGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
10371 ACGTGGCATGCCACGTG
1 ACGTGGCATGCCACGTG
10388 CACAAAAGGA
Statistics
Matches: 92, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 92 1.00
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (31 bp):
ACGTGGCATGCCACGTGTACCAAAAAGTGAC
Found at i:20596 original size:21 final size:21
Alignment explanation
Indices: 20570--20631 Score: 97
Period size: 21 Copynumber: 3.0 Consensus size: 21
20560 TCACACAAAG
20570 AAGTTTCAAGCTCATTGGAGA
1 AAGTTTCAAGCTCATTGGAGA
20591 AAGTTTCAAGCTCATTGGAGA
1 AAGTTTCAAGCTCATTGGAGA
* * *
20612 AGGTATCGAGCTCATTGGAG
1 AAGTTTCAAGCTCATTGGAG
20632 TTGCCTAAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (21 bp):
AAGTTTCAAGCTCATTGGAGA
Found at i:22013 original size:21 final size:21
Alignment explanation
Indices: 21987--22027 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
21977 TTTAAACCCT
21987 ATTGGAGACAAGTGGTACTAA
1 ATTGGAGACAAGTGGTACTAA
* *
22008 ATTGGATATAAGTGGTACTA
1 ATTGGAGACAAGTGGTACTA
22028 GGGTTTATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.07, G:0.27, T:0.29
Consensus pattern (21 bp):
ATTGGAGACAAGTGGTACTAA
Found at i:27033 original size:21 final size:21
Alignment explanation
Indices: 27007--27068 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
26997 TCACACAAAG
27007 AAGTTTCAAGCTCATTGGAGA
1 AAGTTTCAAGCTCATTGGAGA
*
27028 AAGTTTCAAGCTCATTGTAGA
1 AAGTTTCAAGCTCATTGGAGA
*
27049 AGGTTTCAAGCTCATTGGAG
1 AAGTTTCAAGCTCATTGGAG
27069 TTGCCTAAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.31
Consensus pattern (21 bp):
AAGTTTCAAGCTCATTGGAGA
Found at i:28403 original size:26 final size:24
Alignment explanation
Indices: 28374--28434 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 24
28364 TTGATTAATC
* *
28374 TTTACATTTTAGTATTTTACAAGCTG
1 TTTA-ATTTTAG-ACTTCACAAGCTG
*
28400 TTTAGACTTTAGACTTCACAAGCTG
1 TTTA-ATTTTAGACTTCACAAGCTG
28425 TTTAATTTTA
1 TTTAATTTTA
28435 CAAGCTATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 5 0.17
25 15 0.50
26 10 0.33
ACGTcount: A:0.28, C:0.13, G:0.11, T:0.48
Consensus pattern (24 bp):
TTTAATTTTAGACTTCACAAGCTG
Found at i:31372 original size:2 final size:2
Alignment explanation
Indices: 31365--31390 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31355 ATGTATTTAC
31365 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
31391 TAAATAATAA
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
Done.