Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga08g02298.F1
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: 2109
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.27
Found at i:292 original size:12 final size:12
Alignment explanation
Indices: 275--305 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
265 ACTTTCATCT
275 TCTGTCTCTCTG
1 TCTGTCTCTCTG
*
287 TCTGTCTCTTTG
1 TCTGTCTCTCTG
299 TCTGTCT
1 TCTGTCT
306 TTTTCTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.29, G:0.16, T:0.55
Consensus pattern (12 bp):
TCTGTCTCTCTG
Found at i:901 original size:12 final size:12
Alignment explanation
Indices: 886--939 Score: 72
Period size: 12 Copynumber: 4.5 Consensus size: 12
876 ATTGTGATTT
*
886 TGATGAGTTTGG
1 TGATGAGTTTGA
*
898 TGATGAGTTCGA
1 TGATGAGTTTGA
*
910 TGATGAATTTGA
1 TGATGAGTTTGA
*
922 TGATGAGTTCGA
1 TGATGAGTTTGA
934 TGATGA
1 TGATGA
940 TGATGATGAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.26, C:0.04, G:0.33, T:0.37
Consensus pattern (12 bp):
TGATGAGTTTGA
Found at i:913 original size:24 final size:24
Alignment explanation
Indices: 886--939 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
876 ATTGTGATTT
* *
886 TGATGAGTTTGGTGATGAGTTCGA
1 TGATGAATTTGATGATGAGTTCGA
910 TGATGAATTTGATGATGAGTTCGA
1 TGATGAATTTGATGATGAGTTCGA
934 TGATGA
1 TGATGA
940 TGATGATGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.26, C:0.04, G:0.33, T:0.37
Consensus pattern (24 bp):
TGATGAATTTGATGATGAGTTCGA
Found at i:946 original size:24 final size:24
Alignment explanation
Indices: 898--948 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
888 ATGAGTTTGG
*
898 TGATGAGTTCGATGATGAATTTGA
1 TGATGAGTTCGATGATGAATATGA
922 TGATGAGTTCGATGATG-ATGATGA
1 TGATGAGTTCGATGATGAAT-ATGA
946 TGA
1 TGA
949 AGGGGAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 2 0.08
24 23 0.92
ACGTcount: A:0.29, C:0.04, G:0.31, T:0.35
Consensus pattern (24 bp):
TGATGAGTTCGATGATGAATATGA
Found at i:1003 original size:12 final size:12
Alignment explanation
Indices: 962--1005 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
952 GGAATTTGGT
*
962 CATGGTCATGGA
1 CATGGCCATGGA
* *
974 TATGGACATGGA
1 CATGGCCATGGA
*
986 CATGGCCATGGC
1 CATGGCCATGGA
998 CATGGCCA
1 CATGGCCA
1006 CCAAATGCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.25, C:0.23, G:0.32, T:0.20
Consensus pattern (12 bp):
CATGGCCATGGA
Found at i:1545 original size:6 final size:6
Alignment explanation
Indices: 1531--1577 Score: 85
Period size: 6 Copynumber: 7.8 Consensus size: 6
1521 GTGGGGGAGG
*
1531 TGGTAC TGGTGC TGGTGC TGGTGC TGGTGC TGGTGC TGGTGC TGGTG
1 TGGTGC TGGTGC TGGTGC TGGTGC TGGTGC TGGTGC TGGTGC TGGTG
1578 GCAGTAAGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.02, C:0.15, G:0.49, T:0.34
Consensus pattern (6 bp):
TGGTGC
Found at i:1624 original size:12 final size:12
Alignment explanation
Indices: 1622--1657 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
1612 TCGTCAGATG
*
1622 GGTCAAATGGGT
1 GGTCAGATGGGT
1634 GGTCAGATGGGT
1 GGTCAGATGGGT
1646 GGTCAGATGGGT
1 GGTCAGATGGGT
1658 TACAATATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.19, C:0.08, G:0.47, T:0.25
Consensus pattern (12 bp):
GGTCAGATGGGT
Found at i:1645 original size:21 final size:21
Alignment explanation
Indices: 1595--1645 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
1585 GAATATGGGG
*
1595 CAGATGGGCCAAATGGGTCGT
1 CAGATGGGTCAAATGGGTCGT
*
1616 CAGATGGGTCAAATGGGTGGT
1 CAGATGGGTCAAATGGGTCGT
1637 CAGATGGGT
1 CAGATGGGT
1646 GGTCAGATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.24, C:0.14, G:0.41, T:0.22
Consensus pattern (21 bp):
CAGATGGGTCAAATGGGTCGT
Found at i:1671 original size:33 final size:32
Alignment explanation
Indices: 1598--1677 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 32
1588 TATGGGGCAG
*
1598 ATGGGCCAAATGGGTCGTCAGATGGGTCAAAT
1 ATGGGTCAAATGGGTCGTCAGATGGGTCAAAT
** * * *
1630 GGGTGGTCAGATGGGTGGTCAGATGGGTTACAAT
1 ATG-GGTCAAATGGGTCGTCAGATGGGTCA-AAT
1664 ATGGGTCAAATGGG
1 ATGGGTCAAATGGG
1678 CCAAATGGGG
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
32 1 0.03
33 32 0.86
34 4 0.11
ACGTcount: A:0.25, C:0.11, G:0.40, T:0.24
Consensus pattern (32 bp):
ATGGGTCAAATGGGTCGTCAGATGGGTCAAAT
Done.