Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gorai.010G078900.2-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: 2242
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.24
Found at i:1186 original size:12 final size:12
Alignment explanation
Indices: 1125--1177 Score: 67
Period size: 12 Copynumber: 4.7 Consensus size: 12
1115 TGATCATCAT
1125 CAGCAACAGCAG
1 CAGCAACAGCAG
*
1137 CAGCACCAGCAG
1 CAGCAACAGCAG
1149 CAGCAACA--A-
1 CAGCAACAGCAG
*
1158 CAGCAACAGCAA
1 CAGCAACAGCAG
1170 CAGCAACA
1 CAGCAACA
1178 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:1189 original size:6 final size:6
Alignment explanation
Indices: 1125--1177 Score: 58
Period size: 6 Copynumber: 9.3 Consensus size: 6
1115 TGATCATCAT
* * *
1125 CAGCAA CAGCAG CAGCAC CAGCAG CAGC-A -A-CAA CAGCAA CAGCAA
1 CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA
1170 CAGCAA CA
1 CAGCAA CA
1178 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:1355 original size:3 final size:3
Alignment explanation
Indices: 1347--1405 Score: 64
Period size: 3 Copynumber: 19.7 Consensus size: 3
1337 TGAAAGTTTT
* * * * * *
1347 CAG CAG CAG CAG CAG CAG CAG CAG CAT CAA CAA CAG CAG CAA CAA CAA
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
1395 CAG CAG CAG CA
1 CAG CAG CAG CA
1406 ACATTATAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.42, C:0.34, G:0.22, T:0.02
Consensus pattern (3 bp):
CAG
Found at i:1365 original size:15 final size:15
Alignment explanation
Indices: 1350--1408 Score: 82
Period size: 15 Copynumber: 3.9 Consensus size: 15
1340 AAGTTTTCAG
* *
1350 CAGCAGCAGCAGCAG
1 CAGCAGCAGCAACAA
*
1365 CAGCAGCATCAACAA
1 CAGCAGCAGCAACAA
*
1380 CAGCAGCAACAACAA
1 CAGCAGCAGCAACAA
1395 CAGCAGCAGCAACA
1 CAGCAGCAGCAACA
1409 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:1406 original size:18 final size:18
Alignment explanation
Indices: 1359--1408 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
1349 GCAGCAGCAG
* *
1359 CAGCAGCAGCAGCATCAA
1 CAGCAGCAGCAACAACAA
*
1377 CAACAGCAGCAACAACAA
1 CAGCAGCAGCAACAACAA
1395 CAGCAGCAGCAACA
1 CAGCAGCAGCAACA
1409 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:1891 original size:10 final size:9
Alignment explanation
Indices: 1846--1912 Score: 52
Period size: 8 Copynumber: 7.7 Consensus size: 9
1836 TTGGAAAGAG
*
1846 AGAAAGAAC
1 AGAAAGAAA
*
1855 A-AAAGGAA
1 AGAAAGAAA
*
1863 A-AAAGAGA
1 AGAAAGAAA
*
1871 AGAAAGTAA
1 AGAAAGAAA
1880 AGTAAAGAAA
1 AG-AAAGAAA
1890 AGAAAAGAAA
1 AG-AAAGAAA
1900 AG-AAGAAA
1 AGAAAGAAA
1908 A-AAAG
1 AGAAAG
1913 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.