Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017311.1 Corchorus olitorius cultivar O-4 contig17344, 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: 13139
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:163 original size:63 final size:64
Alignment explanation
Indices: 86--274 Score: 153
Period size: 63 Copynumber: 3.0 Consensus size: 64
76 CATTATTTAA
*
86 ACTTTTATAGTTTTACTCAACTAAAAAATCAATTTTTATTTAATTAAATCTAATATCTTTATA-
1 ACTTTTACAGTTTTACTCAACTAAAAAATCAATTTTTATTTAATTAAATCTAATATCTTTATAT
* ** * * * *
149 ATTTTTACCA-TTTTACT-ATTTTAATTAAAA--AACTTATATATATATTAAA---AAAAT-TTT
1 ACTTTTA-CAGTTTTACTCA-ACTAA--AAAATCAATTTTTATTTA-ATTAAATCTAATATCTTT
206 AAATAT
61 --ATAT
* * *
212 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATA
1 ACTTTTACAGTTTTACTCAACTAAAAAATCAATTTTTATTTAATTAAATCTAATATCTTTATA
275 CCTATTTTAT
Statistics
Matches: 92, Mismatches: 18, Indels: 31
0.65 0.13 0.22
Matches are distributed among these distances:
60 3 0.03
61 7 0.08
62 12 0.13
63 49 0.53
64 11 0.12
65 8 0.09
66 2 0.02
ACGTcount: A:0.41, C:0.11, G:0.01, T:0.47
Consensus pattern (64 bp):
ACTTTTACAGTTTTACTCAACTAAAAAATCAATTTTTATTTAATTAAATCTAATATCTTTATAT
Found at i:211 original size:20 final size:20
Alignment explanation
Indices: 172--212 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
162 TACTATTTTA
* *
172 ATTAAAAAACTTATATATAT
1 ATTAAAAAAATTATAAATAT
*
192 ATTAAAAAAATTTTAAATAT
1 ATTAAAAAAATTATAAATAT
212 A
1 A
213 CTTTTACAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTAAAAAAATTATAAATAT
Found at i:366 original size:14 final size:13
Alignment explanation
Indices: 330--368 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
320 TATATATTAG
330 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
343 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
357 AATTTTTTAAAT
1 AATTTTTTAAAT
369 TTTACAATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (13 bp):
AATTTTTTAAATA
Found at i:5741 original size:13 final size:12
Alignment explanation
Indices: 5723--5753 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
5713 AGAGAGAGGA
5723 GGGGGGGGGTAGG
1 GGGGGGGGGT-GG
5736 GGGGGGGGGTGG
1 GGGGGGGGGTGG
5748 GGGGGG
1 GGGGGG
5754 AAGAGCATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.03, C:0.00, G:0.90, T:0.06
Consensus pattern (12 bp):
GGGGGGGGGTGG
Found at i:7079 original size:75 final size:75
Alignment explanation
Indices: 6956--7109 Score: 263
Period size: 75 Copynumber: 2.1 Consensus size: 75
6946 GTTGAGATTA
* * *
6956 CAAACGCATAGGTAGATCCGTACACCGTTACAATACCTACCAAACATCTCTATAAGAATTCAACT
1 CAAACGCACAGGTAGACCCGTACACCGCTACAATACCTACCAAACATCTCTATAAGAATTCAACT
*
7021 ACATATCTAC
66 ACATACCTAC
*
7031 CAAACGCACAGGTAGACCCGTACACCGCTACAATACCTACCAAACATCTCTATGAGAATTCAACT
1 CAAACGCACAGGTAGACCCGTACACCGCTACAATACCTACCAAACATCTCTATAAGAATTCAACT
7096 ACATACCTAC
66 ACATACCTAC
7106 CAAA
1 CAAA
7110 TAAACAAACA
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.39, C:0.31, G:0.10, T:0.21
Consensus pattern (75 bp):
CAAACGCACAGGTAGACCCGTACACCGCTACAATACCTACCAAACATCTCTATAAGAATTCAACT
ACATACCTAC
Found at i:7105 original size:35 final size:35
Alignment explanation
Indices: 6988--7109 Score: 95
Period size: 35 Copynumber: 3.3 Consensus size: 35
6978 CACCGTTACA
*
6988 ATACCTACCAAACATCTCTATAAGAATTCAACTAC
1 ATACCTACCAAACATCTCTATGAGAATTCAACTAC
* * * * * * *
7023 ATATCTACCAAAC-GCAC-AGGTAGACCCGTACACCGCTAC
1 ATACCTACCAAACATCTCTATG-AGA---ATTCA--ACTAC
7062 AATACCTACCAAACATCTCTATGAGAATTCAACTAC
1 -ATACCTACCAAACATCTCTATGAGAATTCAACTAC
7098 ATACCTACCAAA
1 ATACCTACCAAA
7110 TAAACAAACA
Statistics
Matches: 63, Mismatches: 15, Indels: 18
0.66 0.16 0.19
Matches are distributed among these distances:
33 1 0.02
34 5 0.08
35 24 0.38
36 4 0.06
37 3 0.05
38 3 0.05
39 4 0.06
40 12 0.19
41 5 0.08
42 2 0.03
ACGTcount: A:0.40, C:0.31, G:0.07, T:0.21
Consensus pattern (35 bp):
ATACCTACCAAACATCTCTATGAGAATTCAACTAC
Found at i:7172 original size:22 final size:23
Alignment explanation
Indices: 7144--7191 Score: 80
Period size: 22 Copynumber: 2.1 Consensus size: 23
7134 TCACATTCCG
7144 TGAGAGTTGAACCTAA-ACCTCT
1 TGAGAGTTGAACCTAAGACCTCT
*
7166 TGAGAGTTGAATCTAAGACCTCT
1 TGAGAGTTGAACCTAAGACCTCT
7189 TGA
1 TGA
7192 TCTAGGTAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (23 bp):
TGAGAGTTGAACCTAAGACCTCT
Done.