Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017512.1 Corchorus olitorius cultivar O-4 contig17545, 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: 13806
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:4387 original size:119 final size:119
Alignment explanation
Indices: 4176--4419 Score: 461
Period size: 119 Copynumber: 2.0 Consensus size: 119
4166 TAACTTGAAA
4176 TAAAAGGGCCAGAGAATACATATCCATACCAATGAAGCTGAAGTTGATTTATTCAGGCCAATTAT
1 TAAAAGGGCCAGAGAATACATATCCATACCAATGAAGCTGAAGTTGATTTATTCAGGCCAATTAT
4241 AACGGAAGGATATCTCTATCAAAATACTGCATTCAGAGTTGCAGTTCCTGAGAT
66 AACGGAAGGATATCTCTATCAAAATACTGCATTCAGAGTTGCAGTTCCTGAGAT
*
4295 TAAAAGGGCCAGGGAATACATATCCATACCAATGAAGCTGAAGTTGATTTATTCAGGCCAATTAT
1 TAAAAGGGCCAGAGAATACATATCCATACCAATGAAGCTGAAGTTGATTTATTCAGGCCAATTAT
*
4360 AACGGAAGGATATCTCTATCAAAATACTGCATTCAGAGTTGTAGTTCCTGAGAT
66 AACGGAAGGATATCTCTATCAAAATACTGCATTCAGAGTTGCAGTTCCTGAGAT
4414 TGAAAA
1 T-AAAA
4420 TATAGCAACA
Statistics
Matches: 122, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
119 118 0.97
120 4 0.03
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (119 bp):
TAAAAGGGCCAGAGAATACATATCCATACCAATGAAGCTGAAGTTGATTTATTCAGGCCAATTAT
AACGGAAGGATATCTCTATCAAAATACTGCATTCAGAGTTGCAGTTCCTGAGAT
Found at i:9261 original size:2 final size:2
Alignment explanation
Indices: 9254--9286 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
9244 AGCCCACGTC
9254 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9287 AGAGGTCCAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10693 original size:14 final size:13
Alignment explanation
Indices: 10674--10713 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 13
10664 CCTCTCCCTG
10674 TTTTTTTT-GTAT
1 TTTTTTTTGGTAT
10686 ATTTTTTTTGGTA-
1 -TTTTTTTTGGTAT
10699 -TTTTTTTGGTAT
1 TTTTTTTTGGTAT
10711 TTT
1 TTT
10714 CTCCTGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
11 11 0.46
13 10 0.42
14 3 0.12
ACGTcount: A:0.10, C:0.00, G:0.12, T:0.78
Consensus pattern (13 bp):
TTTTTTTTGGTAT
Found at i:10702 original size:11 final size:11
Alignment explanation
Indices: 10688--10713 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
10678 TTTTGTATAT
10688 TTTTTTTGGTA
1 TTTTTTTGGTA
10699 TTTTTTTGGTA
1 TTTTTTTGGTA
10710 TTTT
1 TTTT
10714 CTCCTGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.15, T:0.77
Consensus pattern (11 bp):
TTTTTTTGGTA
Found at i:12131 original size:25 final size:25
Alignment explanation
Indices: 12103--12153 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
12093 ATTTGTATAC
12103 ATGAAATGCAAATTCTATTTATGCT
1 ATGAAATGCAAATTCTATTTATGCT
12128 ATGAAATGCAAATTCTATTTATGCT
1 ATGAAATGCAAATTCTATTTATGCT
12153 A
1 A
12154 ATGAGAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (25 bp):
ATGAAATGCAAATTCTATTTATGCT
Found at i:13336 original size:21 final size:21
Alignment explanation
Indices: 13296--13336 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
13286 TAAGGTTTGG
*
13296 TAGAATTAATAACTTCATTTA
1 TAGAATTAATAACTTAATTTA
13317 TAGAATTAATATA-TTAATTT
1 TAGAATTAATA-ACTTAATTT
13337 TTCTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (21 bp):
TAGAATTAATAACTTAATTTA
Found at i:13802 original size:38 final size:38
Alignment explanation
Indices: 13722--13802 Score: 92
Period size: 38 Copynumber: 2.1 Consensus size: 38
13712 TTCTCTAAAT
* * *
13722 TAAAATATTAATTATCCCAATTGAGATGATTAGACCCT
1 TAAAATATTAATTATCCCAATTCAGATGATGAGACCCA
* * *
13760 TAAAATATTCATTATTCCAATTCAGATGGTGA-ACACCA
1 TAAAATATTAATTATCCCAATTCAGATGATGAGAC-CCA
13798 TAAAA
1 TAAAA
13803 ATTG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
37 2 0.06
38 34 0.94
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (38 bp):
TAAAATATTAATTATCCCAATTCAGATGATGAGACCCA
Done.