Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017666.1 Corchorus olitorius cultivar O-4 contig17699, 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: 12509
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Found at i:2094 original size:16 final size:16
Alignment explanation
Indices: 2070--2105 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
2060 ATTGCCCTGA
*
2070 GTTTTAGGCATGCTCT
1 GTTTCAGGCATGCTCT
2086 GTTTCAGGCATGCTCT
1 GTTTCAGGCATGCTCT
2102 GTTT
1 GTTT
2106 TCGTTAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.19, G:0.25, T:0.44
Consensus pattern (16 bp):
GTTTCAGGCATGCTCT
Found at i:5898 original size:12 final size:12
Alignment explanation
Indices: 5854--5930 Score: 73
Period size: 12 Copynumber: 6.4 Consensus size: 12
5844 TCATCAACTC
*
5854 TTTCAACTACAT
1 TTTCATCTACAT
* *
5866 TTTCATATATAT
1 TTTCATCTACAT
* *
5878 TTTCCTCTAAAT
1 TTTCATCTACAT
5890 TTTCATCTACAT
1 TTTCATCTACAT
*
5902 TTTGATCTACAT
1 TTTCATCTACAT
* * *
5914 TCTCAACAACAT
1 TTTCATCTACAT
5926 TTTCA
1 TTTCA
5931 AATCCATTTT
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 51 1.00
ACGTcount: A:0.30, C:0.22, G:0.01, T:0.47
Consensus pattern (12 bp):
TTTCATCTACAT
Found at i:5985 original size:24 final size:24
Alignment explanation
Indices: 5947--5992 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
5937 TTTTCAACTT
*
5947 CTAAACCAGCTAAATCATCACCTC
1 CTAAACCAGCCAAATCATCACCTC
* *
5971 CTAAACCTGCCAAATTATCACC
1 CTAAACCAGCCAAATCATCACC
5993 CTGAACTACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.37, C:0.37, G:0.04, T:0.22
Consensus pattern (24 bp):
CTAAACCAGCCAAATCATCACCTC
Found at i:6053 original size:24 final size:24
Alignment explanation
Indices: 6026--6077 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
6016 TATCATCAAA
* *
6026 ATTACCTCCTTCTCCATCAGTCTC
1 ATTACCTCCATCTCCATCAGTCCC
* *
6050 ATTACCTCCATCTTCATCATTCCC
1 ATTACCTCCATCTCCATCAGTCCC
6074 ATTA
1 ATTA
6078 TCATCAACAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.38, G:0.02, T:0.38
Consensus pattern (24 bp):
ATTACCTCCATCTCCATCAGTCCC
Found at i:7485 original size:19 final size:19
Alignment explanation
Indices: 7461--7497 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
7451 CTGTTTAGCA
7461 ACTGTACAAATGAGATTAT
1 ACTGTACAAATGAGATTAT
* *
7480 ACTGTACATATTAGATTA
1 ACTGTACAAATGAGATTA
7498 GGTACCGTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.35
Consensus pattern (19 bp):
ACTGTACAAATGAGATTAT
Found at i:7855 original size:8 final size:8
Alignment explanation
Indices: 7842--7887 Score: 92
Period size: 8 Copynumber: 5.8 Consensus size: 8
7832 TTCTTGCTCA
7842 TTGCCAAT
1 TTGCCAAT
7850 TTGCCAAT
1 TTGCCAAT
7858 TTGCCAAT
1 TTGCCAAT
7866 TTGCCAAT
1 TTGCCAAT
7874 TTGCCAAT
1 TTGCCAAT
7882 TTGCCA
1 TTGCCA
7888 TTGCTGACTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 38 1.00
ACGTcount: A:0.24, C:0.26, G:0.13, T:0.37
Consensus pattern (8 bp):
TTGCCAAT
Found at i:12479 original size:1 final size:1
Alignment explanation
Indices: 12473--12509 Score: 65
Period size: 1 Copynumber: 37.0 Consensus size: 1
12463 ATTGTAACCG
*
12473 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.97, C:0.00, G:0.00, T:0.03
Consensus pattern (1 bp):
A
Done.