Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga12g01021.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: 5654
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Found at i:3153 original size:3 final size:3
Alignment explanation
Indices: 3145--3173 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3135 CCCCTTGCCC
3145 CCA CCA CCA CCA CCA CCA CCA CCA CCA CC
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CC
3174 TACTAGACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.69, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:3377 original size:39 final size:39
Alignment explanation
Indices: 3334--3420 Score: 113
Period size: 39 Copynumber: 2.2 Consensus size: 39
3324 TGCCCCTCCT
3334 CCTCCACCTCCACCACC-CTCATTGAAGTCCACTGCCCCA
1 CCTCCACCTCCACCACCGC-CATTGAAGTCCACTGCCCCA
* * * * *
3373 CCTCCACCCCCTCCACCGCCATTGATGTCTAGTGCCCCA
1 CCTCCACCTCCACCACCGCCATTGAAGTCCACTGCCCCA
3412 CCTCCACCT
1 CCTCCACCT
3421 TCATTGCTCC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 40 0.98
40 1 0.02
ACGTcount: A:0.17, C:0.54, G:0.09, T:0.20
Consensus pattern (39 bp):
CCTCCACCTCCACCACCGCCATTGAAGTCCACTGCCCCA
Found at i:3638 original size:31 final size:33
Alignment explanation
Indices: 3603--3671 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
3593 TGGAGAACCA
*
3603 GCACCG-CCCC-CCTCCTATGCGTGGGGCACCT
1 GCACCGCCCCCGCCTCCTATGCGGGGGGCACCT
*
3634 GCACCGCCCCCGCCTCCTATGCGGGGGGCTCCT
1 GCACCGCCCCCGCCTCCTATGCGGGGGGCACCT
*
3667 CCACC
1 GCACC
3672 TCCTCCAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 6 0.18
32 4 0.12
33 23 0.70
ACGTcount: A:0.09, C:0.51, G:0.26, T:0.14
Consensus pattern (33 bp):
GCACCGCCCCCGCCTCCTATGCGGGGGGCACCT
Done.