Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gorai.010G078900.4-JGI_221_v2.1
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: 2758
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Found at i:1705 original size:12 final size:12
Alignment explanation
Indices: 1644--1696 Score: 67
Period size: 12 Copynumber: 4.7 Consensus size: 12
1634 TGATCATCAT
1644 CAGCAACAGCAG
1 CAGCAACAGCAG
*
1656 CAGCACCAGCAG
1 CAGCAACAGCAG
1668 CAGCAACA--A-
1 CAGCAACAGCAG
*
1677 CAGCAACAGCAA
1 CAGCAACAGCAG
1689 CAGCAACA
1 CAGCAACA
1697 TCATCAGCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
9 8 0.22
10 1 0.03
11 1 0.03
12 26 0.72
ACGTcount: A:0.45, C:0.36, G:0.19, T:0.00
Consensus pattern (12 bp):
CAGCAACAGCAG
Found at i:1708 original size:6 final size:6
Alignment explanation
Indices: 1644--1696 Score: 58
Period size: 6 Copynumber: 9.3 Consensus size: 6
1634 TGATCATCAT
* * *
1644 CAGCAA CAGCAG CAGCAC CAGCAG CAGC-A -A-CAA CAGCAA CAGCAA
1 CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA
1689 CAGCAA CA
1 CAGCAA CA
1697 TCATCAGCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 1 0.03
4 2 0.05
5 1 0.03
6 36 0.90
ACGTcount: A:0.45, C:0.36, G:0.19, T:0.00
Consensus pattern (6 bp):
CAGCAA
Found at i:1874 original size:3 final size:3
Alignment explanation
Indices: 1866--1921 Score: 58
Period size: 3 Copynumber: 18.7 Consensus size: 3
1856 TGAAAGTTTT
* * * * * *
1866 CAG CAG CAG CAG CAG CAG CAG CAT CAA CAA CAG CAG CAA CAA CAA CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
1914 CAG CAG CA
1 CAG CAG CA
1922 ACATTATAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.43, C:0.34, G:0.21, T:0.02
Consensus pattern (3 bp):
CAG
Found at i:1884 original size:15 final size:15
Alignment explanation
Indices: 1866--1924 Score: 82
Period size: 15 Copynumber: 3.9 Consensus size: 15
1856 TGAAAGTTTT
* *
1866 CAGCAGCAGCAGCAG
1 CAGCAGCAGCAACAA
*
1881 CAGCAGCATCAACAA
1 CAGCAGCAGCAACAA
*
1896 CAGCAGCAACAACAA
1 CAGCAGCAGCAACAA
1911 CAGCAGCAGCAACA
1 CAGCAGCAGCAACA
1925 TTATAAACTG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.44, C:0.34, G:0.20, T:0.02
Consensus pattern (15 bp):
CAGCAGCAGCAACAA
Found at i:1922 original size:18 final size:18
Alignment explanation
Indices: 1875--1924 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
1865 TCAGCAGCAG
* *
1875 CAGCAGCAGCAGCATCAA
1 CAGCAGCAGCAACAACAA
*
1893 CAACAGCAGCAACAACAA
1 CAGCAGCAGCAACAACAA
1911 CAGCAGCAGCAACA
1 CAGCAGCAGCAACA
1925 TTATAAACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.46, C:0.34, G:0.18, T:0.02
Consensus pattern (18 bp):
CAGCAGCAGCAACAACAA
Found at i:2407 original size:10 final size:9
Alignment explanation
Indices: 2362--2428 Score: 52
Period size: 8 Copynumber: 7.7 Consensus size: 9
2352 TTGGAAAGAG
*
2362 AGAAAGAAC
1 AGAAAGAAA
*
2371 A-AAAGGAA
1 AGAAAGAAA
*
2379 A-AAAGAGA
1 AGAAAGAAA
*
2387 AGAAAGTAA
1 AGAAAGAAA
2396 AGTAAAGAAA
1 AG-AAAGAAA
2406 AGAAAAGAAA
1 AG-AAAGAAA
2416 AG-AAGAAA
1 AGAAAGAAA
2424 A-AAAG
1 AGAAAG
2429 CAGGAAAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
8 22 0.47
9 8 0.17
10 17 0.36
ACGTcount: A:0.73, C:0.01, G:0.22, T:0.03
Consensus pattern (9 bp):
AGAAAGAAA
Done.