Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023161.1 Corchorus olitorius cultivar O-4 contig23194, 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: 19287
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:1696 original size:21 final size:21
Alignment explanation
Indices: 1672--1719 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1662 TGAGATTGTG
1672 AGATTAAACACTGTACAGATC
1 AGATTAAACACTGTACAGATC
*** *
1693 AGATTAGGTACTGTACAGATG
1 AGATTAAACACTGTACAGATC
1714 AGATTA
1 AGATTA
1720 TAATCAGCGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (21 bp):
AGATTAAACACTGTACAGATC
Found at i:2103 original size:6 final size:6
Alignment explanation
Indices: 2092--2141 Score: 50
Period size: 6 Copynumber: 8.0 Consensus size: 6
2082 ACAAGAAGAC
2092 AAGAAA AAGAAA AAGACAAA AAGGAAA AA-AAA GAA-AAA AAGAAA AAGAAA
1 AAGAAA AAGAAA AAG--AAA AA-GAAA AAGAAA -AAGAAA AAGAAA AAGAAA
2142 GAACAGCGCA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.13
6 23 0.59
7 5 0.13
8 5 0.13
9 1 0.03
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:2107 original size:17 final size:16
Alignment explanation
Indices: 2087--2144 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
2077 ATATCACAAG
2087 AAGACAAGAAAAAGAAA
1 AAGA-AAGAAAAAGAAA
* *
2104 AAGACA-AAAAGGAAA
1 AAGAAAGAAAAAGAAA
2119 AA-AAAGAAAAAAAGAAA
1 AAGAAAG--AAAAAGAAA
2136 AAGAAAGAA
1 AAGAAAGAA
2145 CAGCGCATGC
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
14 2 0.06
15 10 0.30
16 3 0.09
17 14 0.42
18 4 0.12
ACGTcount: A:0.79, C:0.03, G:0.17, T:0.00
Consensus pattern (16 bp):
AAGAAAGAAAAAGAAA
Found at i:2124 original size:10 final size:9
Alignment explanation
Indices: 2101--2144 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
2091 CAAGAAAAAG
*
2101 AAAAAGACA
1 AAAAAGAAA
*
2110 AAAAGGAAA
1 AAAAAGAAA
2119 AAAAAG-AA
1 AAAAAGAAA
2127 AAAAAGAAA
1 AAAAAGAAA
2136 AAGAAAGAA
1 AA-AAAGAA
2145 CAGCGCATGC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
8 8 0.27
9 16 0.53
10 6 0.20
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:2124 original size:18 final size:17
Alignment explanation
Indices: 2101--2144 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
2091 CAAGAAAAAG
*
2101 AAAAAGACAAAAAGGAAA
1 AAAAAGA-AAAAAAGAAA
2119 AAAAAGAAAAAAAGAAA
1 AAAAAGAAAAAAAGAAA
2136 AAGAAAGAA
1 AA-AAAGAA
2145 CAGCGCATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAAAAGAAA
Found at i:9809 original size:12 final size:12
Alignment explanation
Indices: 9792--9821 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
9782 GTAACAAGCA
9792 TTTGCCTGATCT
1 TTTGCCTGATCT
9804 TTTGCCTGATCT
1 TTTGCCTGATCT
9816 TGTTGC
1 T-TTGC
9822 TTCTGTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.07, C:0.23, G:0.20, T:0.50
Consensus pattern (12 bp):
TTTGCCTGATCT
Done.