Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g00549.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: 5839
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.33


Found at i:437 original size:42 final size:43

Alignment explanation


    Indices: 389--474  Score: 111
    Period size: 42  Copynumber: 2.0  Consensus size: 43

        379 CTCTTTGGTC

                                    *             *    
        389 TCAAGGCGCAATTTACAGGTTTTCGCCTTGGCCT-TTTTTTTT
          1 TCAAGGCGCAATTTACAGGTTTTCACCTTGGCCTCTTTCTTTT

                     **   * *                          
        431 TCAAGGCGCCCTTTGCGGGTTTTCACCTTGGCCTCTTTCTTTT
          1 TCAAGGCGCAATTTACAGGTTTTCACCTTGGCCTCTTTCTTTT

             
        474 T
          1 T

        475 AGGTAGAATA


Statistics
Matches: 37,  Mismatches: 6, Indels: 1
        0.84            0.14        0.02

Matches are distributed among these distances:
  42   29  0.78
  43    8  0.22

ACGTcount: A:0.10, C:0.26, G:0.20, T:0.44


Consensus pattern (43 bp):   
TCAAGGCGCAATTTACAGGTTTTCACCTTGGCCTCTTTCTTTT

Found at i:5204 original size:5 final size:5

Alignment explanation


    Indices: 5188--5217  Score: 51
    Period size: 5  Copynumber: 5.8  Consensus size: 5

       5178 AACTAAATAA

                                               
       5188 AAAAT GAAAAT AAAAT AAAAT AAAAT AAAA
          1 AAAAT -AAAAT AAAAT AAAAT AAAAT AAAA

       5218 ACTTAAAATG


Statistics
Matches: 24,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   5   19  0.79
   6    5  0.21

ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17


Consensus pattern (5 bp):   
AAAAT

Done.