Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018629.1 Corchorus olitorius cultivar O-4 contig18662, 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: 37501
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:10952 original size:55 final size:55
Alignment explanation
Indices: 10857--10966 Score: 184
Period size: 55 Copynumber: 2.0 Consensus size: 55
10847 TCGATGGATT
* * *
10857 ATTCTTTTTGTTGATATTTCCAAGCTGTAAAGTGTCATTATGGCTAAACATTGGA
1 ATTCTTTTTGTTGATATTTCCAAGCTATAAAGTATAATTATGGCTAAACATTGGA
*
10912 ATTCTTTTTGTTGATATTTCCAAGCTATAAATTATAATTATGGCTAAACATTGGA
1 ATTCTTTTTGTTGATATTTCCAAGCTATAAAGTATAATTATGGCTAAACATTGGA
10967 TAATTATTGG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.43
Consensus pattern (55 bp):
ATTCTTTTTGTTGATATTTCCAAGCTATAAAGTATAATTATGGCTAAACATTGGA
Found at i:12118 original size:2 final size:2
Alignment explanation
Indices: 12111--12175 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
12101 CAATAAATGT
*
12111 AC AC AC AC AC AC AC AC AC AC AC AC AC AC GC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
12153 AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC A
12176 TATATATATA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.49, G:0.02, T:0.00
Consensus pattern (2 bp):
AC
Found at i:12190 original size:14 final size:14
Alignment explanation
Indices: 12173--12201 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
12163 ACACACACAC
12173 ACATATATATATAT
1 ACATATATATATAT
12187 ACATATATATATAT
1 ACATATATATATAT
12201 A
1 A
12202 TACCAACAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
ACATATATATATAT
Found at i:12612 original size:42 final size:42
Alignment explanation
Indices: 12548--12632 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
12538 CTCAGCTTTT
* * *
12548 AATAGTTTAGGTGTAATTATATATTTTCAAGAAAGTAAATTA
1 AATAGTTTAGATGTAATGATATATTTTCAAGAAACTAAATTA
*
12590 AATAGTTTATATGTAATGATATATTTTCAAGAAACTAAATTA
1 AATAGTTTAGATGTAATGATATATTTTCAAGAAACTAAATTA
12632 A
1 A
12633 TAATAGGCAC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.45, C:0.04, G:0.12, T:0.40
Consensus pattern (42 bp):
AATAGTTTAGATGTAATGATATATTTTCAAGAAACTAAATTA
Found at i:14671 original size:55 final size:55
Alignment explanation
Indices: 14587--14696 Score: 177
Period size: 55 Copynumber: 2.0 Consensus size: 55
14577 TCGGTGGATC
* *
14587 ATTCTTTTTGTTGATATTGTCAAGCTGTAAAGTGTAATTATGGGTAAACATTGGA
1 ATTCTTTTTGTTGATATTGTCAAGCTGTAAAGTATAATTATGGCTAAACATTGGA
*
14642 ATTCTTTTTGTTGATATT-TCCAAGCTGTAAATTATAATTATGGCTAAACATTGGA
1 ATTCTTTTTGTTGATATTGT-CAAGCTGTAAAGTATAATTATGGCTAAACATTGGA
14697 TAAATATTAG
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
54 1 0.02
55 50 0.98
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (55 bp):
ATTCTTTTTGTTGATATTGTCAAGCTGTAAAGTATAATTATGGCTAAACATTGGA
Found at i:20664 original size:3 final size:3
Alignment explanation
Indices: 20656--20683 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
20646 TCACAGAAGT
20656 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
20684 GAAATGGGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:23416 original size:26 final size:26
Alignment explanation
Indices: 23382--23437 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
23372 TTTGACTTTA
23382 ATCATTTAAACACTTTCCAATAATTC
1 ATCATTTAAACACTTTCCAATAATTC
23408 ATCATTTAAACACTTTCCAATAATTC
1 ATCATTTAAACACTTTCCAATAATTC
23434 ATCA
1 ATCA
23438 ATGGACATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.38
Consensus pattern (26 bp):
ATCATTTAAACACTTTCCAATAATTC
Found at i:24011 original size:6 final size:6
Alignment explanation
Indices: 24000--24028 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
23990 TTACAAGCTC
24000 CCTTCT CCTTCT CCTTCT CCTTCT -CTTCT
1 CCTTCT CCTTCT CCTTCT CCTTCT CCTTCT
24029 TTTTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (6 bp):
CCTTCT
Done.