Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga12g01023.F2
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: 3254
ACGTcount: A:0.26, C:0.13, G:0.31, T:0.30
Found at i:1021 original size:6 final size:6
Alignment explanation
Indices: 1005--1034 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
995 GTGGGTGTTT
*
1005 CTGGTG TTGGTG CTGGTG CTGGTG CTGGTG
1 CTGGTG CTGGTG CTGGTG CTGGTG CTGGTG
1035 TTGGCCCTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.13, G:0.50, T:0.37
Consensus pattern (6 bp):
CTGGTG
Found at i:1022 original size:12 final size:12
Alignment explanation
Indices: 1005--1053 Score: 62
Period size: 12 Copynumber: 4.1 Consensus size: 12
995 GTGGGTGTTT
1005 CTGGTGTTGGTG
1 CTGGTGTTGGTG
*
1017 CTGGTGCTGGTG
1 CTGGTGTTGGTG
**
1029 CTGGTGTTGGCC
1 CTGGTGTTGGTG
*
1041 CTGGAGTTGGTG
1 CTGGTGTTGGTG
1053 C
1 C
1054 AAGTGGTGGT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.02, C:0.16, G:0.47, T:0.35
Consensus pattern (12 bp):
CTGGTGTTGGTG
Found at i:1028 original size:18 final size:18
Alignment explanation
Indices: 1005--1053 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
995 GTGGGTGTTT
**
1005 CTGGTGTTGGTGCTGGTG
1 CTGGTGTTGGTGCTGGCC
* *
1023 CTGGTGCTGGTGTTGGCC
1 CTGGTGTTGGTGCTGGCC
*
1041 CTGGAGTTGGTGC
1 CTGGTGTTGGTGC
1054 AAGTGGTGGT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.02, C:0.16, G:0.47, T:0.35
Consensus pattern (18 bp):
CTGGTGTTGGTGCTGGCC
Found at i:2261 original size:24 final size:24
Alignment explanation
Indices: 2234--2280 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
2224 CTCTAGAGAT
* * *
2234 CGTGACCGTGATCGTGATAGGGAG
1 CGTGACCGAGATAGGGATAGGGAG
*
2258 CGTGATCGAGATAGGGATAGGGA
1 CGTGACCGAGATAGGGATAGGGA
2281 TCGATATAGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.13, G:0.43, T:0.19
Consensus pattern (24 bp):
CGTGACCGAGATAGGGATAGGGAG
Found at i:2263 original size:18 final size:18
Alignment explanation
Indices: 2240--2274 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2230 AGATCGTGAC
*
2240 CGTGATCGTGATAGGGAG
1 CGTGATCGAGATAGGGAG
2258 CGTGATCGAGATAGGGA
1 CGTGATCGAGATAGGGA
2275 TAGGGATCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.11, G:0.43, T:0.20
Consensus pattern (18 bp):
CGTGATCGAGATAGGGAG
Found at i:2888 original size:3 final size:3
Alignment explanation
Indices: 2880--2912 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2870 ATTAACACTT
2880 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
2913 CTTTAGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:3035 original size:18 final size:18
Alignment explanation
Indices: 3012--3065 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
3002 CTGTTGGCTG
3012 TTTTGTTGTATTATTTAT
1 TTTTGTTGTATTATTTAT
*
3030 TTTTGTCCTTTATT-TTTAT
1 TTTTGT--TGTATTATTTAT
*
3049 TTTTATTGTTATTATTT
1 TTTTGTTG-TATTATTT
3066 TTGGCTTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
17 1 0.03
18 10 0.34
19 13 0.45
20 5 0.17
ACGTcount: A:0.15, C:0.04, G:0.07, T:0.74
Consensus pattern (18 bp):
TTTTGTTGTATTATTTAT
Done.