Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga12g00587.N1

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: 1925
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36


Found at i:983 original size:19 final size:18

Alignment explanation


    Indices: 959--1001  Score: 52
    Period size: 19  Copynumber: 2.3  Consensus size: 18

        949 TCCGCTTCAA

                           *    
        959 TTTTAAT-TTTGTTACTTAT
          1 TTTTAATATTT-TTAATT-T

                              
        978 TTTTAATATTTTTAATTT
          1 TTTTAATATTTTTAATTT

                  
        996 TTTTAA
          1 TTTTAA

       1002 AGTCAAGTAA


Statistics
Matches: 22,  Mismatches: 1, Indels: 3
        0.85            0.04        0.12

Matches are distributed among these distances:
  18    7  0.32
  19   12  0.55
  20    3  0.14

ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70


Consensus pattern (18 bp):   
TTTTAATATTTTTAATTT

Found at i:1683 original size:42 final size:40

Alignment explanation


    Indices: 1599--1683  Score: 109
    Period size: 43  Copynumber: 2.1  Consensus size: 40

       1589 TAATTTTTCA

                                                 *  
       1599 AAAAATTAAAAAAACTATTTTTATGATTTAAAAATTATTT
          1 AAAAATTAAAAAAACTATTTTTATGATTTAAAAATTAATT

                                       **              
       1639 AAAAATTATAAAAAACTATTTTTTTATTTTTTAAAAA-TAATT
          1 AAAAATTA-AAAAAACTA--TTTTTATGATTTAAAAATTAATT

               
       1681 AAA
          1 AAA

       1684 TGCTAGTGTG


Statistics
Matches: 39,  Mismatches: 3, Indels: 4
        0.85            0.07        0.09

Matches are distributed among these distances:
  40    8  0.21
  41    9  0.23
  42    7  0.18
  43   15  0.38

ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44


Consensus pattern (40 bp):   
AAAAATTAAAAAAACTATTTTTATGATTTAAAAATTAATT
Done.