Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013968.1 Corchorus olitorius cultivar O-4 contig14001, 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: 17797
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:195 original size:45 final size:45
Alignment explanation
Indices: 134--223 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
124 TTATCTAAAT
*
134 TACTACTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTA
1 TACTACTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTA
* *
179 TACTCCTCCATTTCTAGATAATTCATCAAAATAAAGCTAATATTA
1 TACTACTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTA
224 ATTGTTGCTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.40, C:0.20, G:0.06, T:0.34
Consensus pattern (45 bp):
TACTACTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTA
Found at i:1830 original size:3 final size:3
Alignment explanation
Indices: 1824--1888 Score: 121
Period size: 3 Copynumber: 21.7 Consensus size: 3
1814 AAAAAAAAGT
*
1824 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1872 AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AA
1889 AAGGCCATTT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3237 original size:13 final size:12
Alignment explanation
Indices: 3221--3262 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
3211 TTTACTGTTT
3221 TTTTATTTAAATG
1 TTTTA-TTAAATG
*
3234 TTTTATAAAATG
1 TTTTATTAAATG
3246 TTTTATTAAATTG
1 TTTTATTAAA-TG
3259 TTTT
1 TTTT
3263 GGGTGCATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 15 0.58
13 11 0.42
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (12 bp):
TTTTATTAAATG
Found at i:3246 original size:12 final size:13
Alignment explanation
Indices: 3221--3262 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
3211 TTTACTGTTT
*
3221 TTTTATTTAAATG
1 TTTTATTAAAATG
3234 TTTTA-TAAAATG
1 TTTTATTAAAATG
*
3246 TTTTATTAAATTG
1 TTTTATTAAAATG
3259 TTTT
1 TTTT
3263 GGGTGCATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (13 bp):
TTTTATTAAAATG
Found at i:7629 original size:20 final size:20
Alignment explanation
Indices: 7606--7645 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
7596 AGGAAAAGTT
*
7606 TAAATTAAAAAATTATATAA
1 TAAATTAAAAAATGATATAA
**
7626 TAAATTGTAAAATGATATAA
1 TAAATTAAAAAATGATATAA
7646 ATTTAAAAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (20 bp):
TAAATTAAAAAATGATATAA
Found at i:8123 original size:3 final size:3
Alignment explanation
Indices: 8117--8157 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
8107 ATAGTAGTAC
8117 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
8158 GTTTTACACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:9409 original size:2 final size:2
Alignment explanation
Indices: 9404--9524 Score: 233
Period size: 2 Copynumber: 60.5 Consensus size: 2
9394 TAGACACATT
9404 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
9446 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
9488 AG AG AG AG AG AG AG AG AG AG AG AG GG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
9525 CGGTTAAATT
Statistics
Matches: 117, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 117 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:10967 original size:19 final size:18
Alignment explanation
Indices: 10943--10978 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
10933 TGAAGACTTA
10943 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
10962 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
10979 ATTATCTCAA
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
Done.