Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga14g00676.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: 5603
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:2640 original size:72 final size:70
Alignment explanation
Indices: 2508--2641 Score: 162
Period size: 72 Copynumber: 1.9 Consensus size: 70
2498 TTAGGGCCTA
* * **
2508 AACTTTTTTTATCTAAGTTAGACCCTGAACTTGACAATTATTCTCACATTAAGGTTTGAATTGGG
1 AACTTTTTTTATCCAAGTTAGACCCTGAACTGGACAATTATTCTCACATTAAGGCCTGAATTGGG
2573 GCTTG
66 GCTTG
* * * *
2578 AACTTCTTTTTAGTCCAAGTTAG-CTCTTGAACTGGACAATTATTCTGATATTGAGGCCTGAATT
1 AACTT-TTTTTA-TCCAAGTTAGAC-CCTGAACTGGACAATTATTCTCACATTAAGGCCTGAATT
2642 TTATGGTTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
70 5 0.09
71 7 0.13
72 41 0.77
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (70 bp):
AACTTTTTTTATCCAAGTTAGACCCTGAACTGGACAATTATTCTCACATTAAGGCCTGAATTGGG
GCTTG
Found at i:3517 original size:65 final size:68
Alignment explanation
Indices: 3442--3573 Score: 173
Period size: 68 Copynumber: 2.0 Consensus size: 68
3432 AATTAGGTCT
* * *
3442 ATTTTCGTACCTGTA-TTTTTT-TT-TTTTAGTA-CTCGAACTTGATAACTAAGTCTATTTTAAT
1 ATTTTCGTACCTATATTTTTTTATTATTTTAGTACCT-GAACTTGACAACTAAATCTATTTTAAT
3503 CCTC
65 CCTC
* * *
3507 ATTTTTGTACCTATATTTTTTTATTATTTTGGTACCTGAACTTGGCAACTAAATCTATTTTAATC
1 ATTTTCGTACCTATATTTTTTTATTATTTTAGTACCTGAACTTGACAACTAAATCTATTTTAATC
3572 CT
66 CT
3574 TGCACTTGAC
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
65 13 0.23
66 6 0.11
67 2 0.04
68 34 0.60
69 2 0.04
ACGTcount: A:0.24, C:0.16, G:0.09, T:0.51
Consensus pattern (68 bp):
ATTTTCGTACCTATATTTTTTTATTATTTTAGTACCTGAACTTGACAACTAAATCTATTTTAATC
CTC
Done.