Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga05g04038.N3
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: 3994
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Found at i:2754 original size:201 final size:201
Alignment explanation
Indices: 2397--2802 Score: 643
Period size: 201 Copynumber: 2.0 Consensus size: 201
2387 GAAATTACTA
* **
2397 AGAATGACTCTAGTCTTTGTTGCTGCCCCAAATTGAGAATTCTTCAGATATGCCATTGCAAAAGT
1 AGAATGACTCTAGTCTTTGTTGCTACCCCAAATTGAGAATTCTTCAGATAAACCATTGCAAAAGT
* * *
2462 TTAAAATATGTTTGTGCAAACACTTCTGCTCAAGAGCTTCAATCATTGGAATCTATCACAATAAT
66 TTAAAATACGTTTGTGCAAACACTACTGCTCAAGAGCTGCAATCATTGGAATCTATCACAATAAT
*
2527 TGGTTGTCCTCAACTTATGCAAATCTTCAAGATGGAACAAAATGAGAATGGGCAAGATGTTGTGG
131 TGGTTGTCCTCAACTTATGCAAATCTTCAAGATGGAACAAAATGAGAATAGGCAAGATGTTGTGG
2592 TTCCTC
196 TTCCTC
* * * * * * *
2598 AGAATGGCTCTTGTCTTTGTTGCTATCCGAAATTGAGAATTCTTGAGATAAACCGTTGCGAAAGT
1 AGAATGACTCTAGTCTTTGTTGCTACCCCAAATTGAGAATTCTTCAGATAAACCATTGCAAAAGT
* *
2663 TTAAAATACGTTTGTGCAAACACTAC-GACTCAAGGGCTGCAATCATTGGAATCTGTCACAATAA
66 TTAAAATACGTTTGTGCAAACACTACTG-CTCAAGAGCTGCAATCATTGGAATCTATCACAATAA
*
2727 TTGGTTGTCCTCAACTTATGCAAATCTTCAAGATGGAACAAAATGAGCATAGGCAAGATGTTGTG
130 TTGGTTGTCCTCAACTTATGCAAATCTTCAAGATGGAACAAAATGAGAATAGGCAAGATGTTGTG
2792 GTTCCTC
195 GTTCCTC
2799 AGAA
1 AGAA
2803 CCAATATTGC
Statistics
Matches: 187, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
200 1 0.01
201 186 0.99
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31
Consensus pattern (201 bp):
AGAATGACTCTAGTCTTTGTTGCTACCCCAAATTGAGAATTCTTCAGATAAACCATTGCAAAAGT
TTAAAATACGTTTGTGCAAACACTACTGCTCAAGAGCTGCAATCATTGGAATCTATCACAATAAT
TGGTTGTCCTCAACTTATGCAAATCTTCAAGATGGAACAAAATGAGAATAGGCAAGATGTTGTGG
TTCCTC
Found at i:3901 original size:11 final size:11
Alignment explanation
Indices: 3885--3921 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
3875 CTAACACGAG
3885 TTTTTTTTTAC
1 TTTTTTTTTAC
3896 TTTTTTTTTAC
1 TTTTTTTTTAC
*
3907 TTTTTTTTTTC
1 TTTTTTTTTAC
3918 TTTT
1 TTTT
3922 ATATATTTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.05, C:0.08, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTTTTAC
Done.