Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga10g00725.P2
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: 11750
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.29
Found at i:3131 original size:12 final size:12
Alignment explanation
Indices: 3114--3144 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
3104 ACTCGGGGAA
3114 GAGGCCGTGGTC
1 GAGGCCGTGGTC
3126 GAGGCCGTGGTC
1 GAGGCCGTGGTC
3138 GAGGCCG
1 GAGGCCG
3145 AGGTAGTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.10, C:0.26, G:0.52, T:0.13
Consensus pattern (12 bp):
GAGGCCGTGGTC
Found at i:4366 original size:12 final size:12
Alignment explanation
Indices: 4349--4379 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
4339 ACTCGGGGAA
4349 GAGGCCGTGGTC
1 GAGGCCGTGGTC
4361 GAGGCCGTGGTC
1 GAGGCCGTGGTC
4373 GAGGCCG
1 GAGGCCG
4380 AGGTAGTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.10, C:0.26, G:0.52, T:0.13
Consensus pattern (12 bp):
GAGGCCGTGGTC
Found at i:9250 original size:51 final size:52
Alignment explanation
Indices: 9195--9328 Score: 236
Period size: 51 Copynumber: 2.6 Consensus size: 52
9185 TGATACAAAT
* *
9195 TGATAATAGGTTAGGTAAATGTTTCATGATAATG-GTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCATGATAATGTATTAGGTAAATGTTTCA
9246 TGATAATGGGTTAGGTAAATGTTT-ATGATAATGTATTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCATGATAATGTATTAGGTAAATGTTTCA
9297 TGATAATGGGTTAGGTAAATGTTTCATGATAA
1 TGATAATGGGTTAGGTAAATGTTTCATGATAA
9329 GAATTTCATG
Statistics
Matches: 79, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
50 9 0.11
51 63 0.80
52 7 0.09
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.40
Consensus pattern (52 bp):
TGATAATGGGTTAGGTAAATGTTTCATGATAATGTATTAGGTAAATGTTTCA
Found at i:9264 original size:26 final size:26
Alignment explanation
Indices: 9195--9328 Score: 227
Period size: 26 Copynumber: 5.2 Consensus size: 26
9185 TGATACAAAT
*
9195 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
9221 TGATAAT-GGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
9246 TGATAATGGGTTAGGTAAATGTTT-A
1 TGATAATGGGTTAGGTAAATGTTTCA
**
9271 TGATAATGTATTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
9297 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
9323 TGATAA
1 TGATAA
9329 GAATTTCATG
Statistics
Matches: 102, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
25 48 0.47
26 54 0.53
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.40
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Done.