Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012122.1 Corchorus olitorius cultivar O-4 contig12155, 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: 28242
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Found at i:5746 original size:19 final size:18
Alignment explanation
Indices: 5722--5757 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
5712 TGAAGACTTA
5722 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
5741 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
5758 ATTATCTCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:13184 original size:31 final size:32
Alignment explanation
Indices: 13117--13181 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
13107 TTTGGCGCCG
13117 TTGCCGGGGAAGGAAAACTTTCTCCTGGTTTT
1 TTGCCGGGGAAGGAAAACTTTCTCCTGGTTTT
13149 TTGCCGGGGAAGGAAAACTTTCTCCTGGTTTT
1 TTGCCGGGGAAGGAAAACTTTCTCCTGGTTTT
13181 T
1 T
13182 GCCTAGGAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.35
Consensus pattern (32 bp):
TTGCCGGGGAAGGAAAACTTTCTCCTGGTTTT
Found at i:13191 original size:31 final size:32
Alignment explanation
Indices: 13117--13191 Score: 116
Period size: 32 Copynumber: 2.4 Consensus size: 32
13107 TTTGGCGCCG
*
13117 TTGCCGGGGAAGGAAAACTTTCTCCTGGTTTT
1 TTGCCGAGGAAGGAAAACTTTCTCCTGGTTTT
*
13149 TTGCCGGGGAAGGAAAACTTTCTCCTGG-TTT
1 TTGCCGAGGAAGGAAAACTTTCTCCTGGTTTT
*
13180 TTGCCTAGGAAG
1 TTGCCGAGGAAG
13192 TAAGGAATCG
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 13 0.32
32 28 0.68
ACGTcount: A:0.20, C:0.19, G:0.29, T:0.32
Consensus pattern (32 bp):
TTGCCGAGGAAGGAAAACTTTCTCCTGGTTTT
Found at i:16201 original size:21 final size:21
Alignment explanation
Indices: 16157--16229 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
16147 CCACTACCAA
* **
16157 GCCACAACCGGCCATTCACCGT
1 GCCACCACCGGCCAAGC-CCGT
**
16179 GCCACCACCGGTTAAGCCCGT
1 GCCACCACCGGCCAAGCCCGT
*
16200 GCCACCACCGGCCATGCCCGT
1 GCCACCACCGGCCAAGCCCGT
*
16221 GCCATCACC
1 GCCACCACC
16230 ATTCCAAGCC
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
21 30 0.71
22 12 0.29
ACGTcount: A:0.19, C:0.48, G:0.21, T:0.12
Consensus pattern (21 bp):
GCCACCACCGGCCAAGCCCGT
Found at i:22979 original size:32 final size:30
Alignment explanation
Indices: 22894--22966 Score: 105
Period size: 30 Copynumber: 2.4 Consensus size: 30
22884 GGCTTCAAAT
*
22894 GTGTGTGTGAAAT-TCATTGGG-CCTCTTTTA
1 GTGTGTGTGAAGTAT-ATTGGGCCCT-TTTTA
22924 GTGTGTGTGAAGTATATTGGGCCCTTTTTA
1 GTGTGTGTGAAGTATATTGGGCCCTTTTTA
22954 GTGTGTGTGAAGT
1 GTGTGTGTGAAGT
22967 GTGTTGGTGG
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
30 36 0.90
31 4 0.10
ACGTcount: A:0.16, C:0.10, G:0.32, T:0.42
Consensus pattern (30 bp):
GTGTGTGTGAAGTATATTGGGCCCTTTTTA
Found at i:26682 original size:20 final size:20
Alignment explanation
Indices: 26657--26698 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
26647 ACTAAAATCT
*
26657 AAATAATTAATGGGTTCTAC
1 AAATAATTAATGCGTTCTAC
26677 AAATAATTAATGCGTTCTAC
1 AAATAATTAATGCGTTCTAC
26697 AA
1 AA
26699 GATCTTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (20 bp):
AAATAATTAATGCGTTCTAC
Done.