Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020337.1 Corchorus olitorius cultivar O-4 contig20370, 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: 18336
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:88 original size:30 final size:31
Alignment explanation
Indices: 54--113 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 31
44 TTTTAAATTT
*
54 AAAAACGCAAAACAATTTTTTTTA-TGACGC
1 AAAAACACAAAACAATTTTTTTTATTGACGC
84 AAAAACACAAAACAATTTTTTTTATTGACG
1 AAAAACACAAAACAATTTTTTTTATTGACG
114 ACGCAAAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 23 0.82
31 5 0.18
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32
Consensus pattern (31 bp):
AAAAACACAAAACAATTTTTTTTATTGACGC
Found at i:524 original size:15 final size:16
Alignment explanation
Indices: 500--539 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
490 AGAGGTTGAA
*
500 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
515 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
531 AGAAAACAA
1 AGAAAACAA
540 AGCAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:9004 original size:31 final size:32
Alignment explanation
Indices: 8948--9015 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 32
8938 GTTTTCTCAT
*
8948 GTCATTCGGGTTTCGGCTCATCTGGATTCA-G
1 GTCATTCGGGTCTCGGCTCATCTGGATTCAGG
* *
8979 GTCATTCGGGTCTCGGGTC-TGCTGGATTTAGG
1 GTCATTCGGGTCTCGGCTCAT-CTGGATTCAGG
9011 GTCAT
1 GTCAT
9016 GCAGGTTCGG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 1 0.03
31 25 0.78
32 6 0.19
ACGTcount: A:0.12, C:0.21, G:0.32, T:0.35
Consensus pattern (32 bp):
GTCATTCGGGTCTCGGCTCATCTGGATTCAGG
Found at i:9026 original size:31 final size:31
Alignment explanation
Indices: 8969--9027 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
8959 TTCGGCTCAT
* *
8969 CTGGATTCAGGTCATTCGGGTCTCGGGTCTG
1 CTGGATTCAGGTCATGCAGGTCTCGGGTCTG
*
9000 CTGGATTTAGGGTCATGCAGGT-TCGGGT
1 CTGGATTCA-GGTCATGCAGGTCTCGGGT
9028 TTTGGCCTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 14 0.58
32 10 0.42
ACGTcount: A:0.12, C:0.19, G:0.37, T:0.32
Consensus pattern (31 bp):
CTGGATTCAGGTCATGCAGGTCTCGGGTCTG
Found at i:9154 original size:26 final size:23
Alignment explanation
Indices: 9108--9154 Score: 58
Period size: 26 Copynumber: 1.9 Consensus size: 23
9098 TTGGGTCAGC
*
9108 CTTAAATTTTTAAATGTTTAATT
1 CTTAAATTTTTAAATGGTTAATT
9131 CTTAAATTTATTTAAAATGGTTAA
1 CTTAAA-TT-TTT-AAATGGTTAA
9155 AATTATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 2 0.10
25 3 0.15
26 9 0.45
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.51
Consensus pattern (23 bp):
CTTAAATTTTTAAATGGTTAATT
Found at i:10729 original size:5 final size:5
Alignment explanation
Indices: 10707--10749 Score: 68
Period size: 5 Copynumber: 8.2 Consensus size: 5
10697 TAATGTTTAG
10707 ATATA TATATA TATATA ATATA ATATA ATATA ATATA ATATA A
1 ATATA -ATATA -ATATA ATATA ATATA ATATA ATATA ATATA A
10750 ATCATCATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 26 0.70
6 11 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:14669 original size:11 final size:11
Alignment explanation
Indices: 14640--14671 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
14630 ATTTCATTAC
*
14640 ATACATACATT
1 ATACATATATT
14651 ATACATATATT
1 ATACATATATT
14662 ATACATATAT
1 ATACATATAT
14672 AATATTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (11 bp):
ATACATATATT
Found at i:18222 original size:2 final size:2
Alignment explanation
Indices: 18215--18248 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
18205 TTTTATTCAC
18215 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18249 CTGACAACAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.