Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016246.1 Corchorus olitorius cultivar O-4 contig16279, 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: 55198
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:3909 original size:48 final size:49
Alignment explanation
Indices: 3851--3955 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 49
3841 AAGGAACAAT
***
3851 AAAAAGTAAAACATCAATTTTATCTTAAAAATTGAGAAAAAGTGCAACG
1 AAAAAGTAAAACATCAATTTTATAGCAAAAATTGAGAAAAAGTGCAACG
* *
3900 AAAAA-TAAAAGATCAATTTTGTAGCAAAAATTGAGAAAAAGTGC-A-G
1 AAAAAGTAAAACATCAATTTTATAGCAAAAATTGAGAAAAAGTGCAACG
3946 -AAAAGTAAAA
1 AAAAAGTAAAA
3956 GATTGCTTTG
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
45 4 0.08
46 6 0.12
47 1 0.02
48 34 0.68
49 5 0.10
ACGTcount: A:0.56, C:0.08, G:0.14, T:0.22
Consensus pattern (49 bp):
AAAAAGTAAAACATCAATTTTATAGCAAAAATTGAGAAAAAGTGCAACG
Found at i:5227 original size:9 final size:9
Alignment explanation
Indices: 5207--5235 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
5197 TTAATTCATT
5207 TAATTTCC-
1 TAATTTCCA
5215 TAATTTCCA
1 TAATTTCCA
5224 TAATTTCCA
1 TAATTTCCA
5233 TAA
1 TAA
5236 GTAATTTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (9 bp):
TAATTTCCA
Found at i:8177 original size:20 final size:21
Alignment explanation
Indices: 8154--8192 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
8144 TTTTTTGCGC
8154 GGAGCAAGTTTTT-AGATGCA
1 GGAGCAAGTTTTTAAGATGCA
**
8174 GGAGCTGGTTTTTAAGATG
1 GGAGCAAGTTTTTAAGATG
8193 AGTGATATCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.26, C:0.08, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAGCAAGTTTTTAAGATGCA
Found at i:9569 original size:56 final size:56
Alignment explanation
Indices: 9497--9610 Score: 201
Period size: 56 Copynumber: 2.0 Consensus size: 56
9487 TTTATTTTGT
* * *
9497 AGAATAATTAAGTAGAGATCGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAGGGGGATAAGATTTATTATAACATTTATTATGTGAA
9553 AGAATAATTAAGTAGAGATAGGGGGATAAGATTTATTATAACATTTATTATGTGAA
1 AGAATAATTAAGTAGAGATAGGGGGATAAGATTTATTATAACATTTATTATGTGAA
9609 AG
1 AG
9611 GAAACAGATA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.33
Consensus pattern (56 bp):
AGAATAATTAAGTAGAGATAGGGGGATAAGATTTATTATAACATTTATTATGTGAA
Found at i:10997 original size:13 final size:13
Alignment explanation
Indices: 10979--11004 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10969 AAAGTAACAA
10979 CAAAAATCATCAC
1 CAAAAATCATCAC
10992 CAAAAATCATCAC
1 CAAAAATCATCAC
11005 TCATGCCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (13 bp):
CAAAAATCATCAC
Found at i:12581 original size:22 final size:22
Alignment explanation
Indices: 12532--12582 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
12522 AAATATTACC
* **
12532 ATAATTATTTTTGGCAGCCATA
1 ATAATTATTTTTGCCAGAAATA
12554 ATAATTATTTTTGCCAAGAAATA
1 ATAATTATTTTTGCC-AGAAATA
12577 A-AATTA
1 ATAATTA
12583 GGGATTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (22 bp):
ATAATTATTTTTGCCAGAAATA
Found at i:42418 original size:23 final size:23
Alignment explanation
Indices: 42392--42444 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
42382 AGTTTTCAAG
*
42392 TCATTTATAATTATTGG-ATTTGA
1 TCATTTATAA-TATAGGAATTTGA
42415 TCATTGT-TAATATAGGAATTTGA
1 TCATT-TATAATATAGGAATTTGA
*
42438 TTATTTA
1 TCATTTA
42445 AGAAACAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
22 6 0.24
23 18 0.72
24 1 0.04
ACGTcount: A:0.32, C:0.04, G:0.13, T:0.51
Consensus pattern (23 bp):
TCATTTATAATATAGGAATTTGA
Found at i:48745 original size:30 final size:31
Alignment explanation
Indices: 48711--48776 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 31
48701 ATTCATAAAA
48711 AGTTTAATTTGGTGAGGTAGGGTGTAAA-TT
1 AGTTTAATTTGGTGAGGTAGGGTGTAAACTT
48741 AGTTTAATTTGGTGAGGTAGGGTGTAAACTT
1 AGTTTAATTTGGTGAGGTAGGGTGTAAACTT
48772 AGTTT
1 AGTTT
48777 TTGTTTTAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 28 0.80
31 7 0.20
ACGTcount: A:0.26, C:0.02, G:0.32, T:0.41
Consensus pattern (31 bp):
AGTTTAATTTGGTGAGGTAGGGTGTAAACTT
Found at i:50249 original size:21 final size:21
Alignment explanation
Indices: 50223--50268 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
50213 CATTCAAATG
*
50223 AAATCACATCAATAAAACTTA
1 AAATCACATCAATAAAACTCA
50244 AAATCACATCAATAAAACTCA
1 AAATCACATCAATAAAACTCA
50265 AAAT
1 AAAT
50269 TATAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.59, C:0.20, G:0.00, T:0.22
Consensus pattern (21 bp):
AAATCACATCAATAAAACTCA
Done.