Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_03632

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, 966

Length: 1611
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.25


Found at i:835 original size:18 final size:17

Alignment explanation


    Indices: 804--838  Score: 52
    Period size: 18  Copynumber: 2.0  Consensus size: 17

        794 AAGGATGGTT

                             
        804 AGATGATGAGCCTGAGG
          1 AGATGATGAGCCTGAGG

                      *       
        821 AGATAGATGATCCTGAGG
          1 AGAT-GATGAGCCTGAGG

        839 CAACCAAGCC


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  17    4  0.25
  18   12  0.75

ACGTcount: A:0.31, C:0.11, G:0.37, T:0.20


Consensus pattern (17 bp):   
AGATGATGAGCCTGAGG

Found at i:1539 original size:3 final size:3

Alignment explanation


    Indices: 1531--1562  Score: 64
    Period size: 3  Copynumber: 10.7  Consensus size: 3

       1521 AGAAAAGGCT

                                                      
       1531 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
          1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA

       1563 GAAAGAAGGA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   29  1.00

ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00


Consensus pattern (3 bp):   
GAA

Done.