Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_34589

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: 3192
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25


Found at i:1592 original size:42 final size:42

Alignment explanation


    Indices: 1546--1637  Score: 105
    Period size: 42  Copynumber: 2.2  Consensus size: 42

       1536 GTCACCCCTT

                  *                       *            
       1546 AGTTATCGAAGACA-GTCAAGGTCAAAGTCTAGATCACCAATC
          1 AGTTATAGAAGA-AGGTCAAGGTCAAAGTCAAGATCACCAATC

                    **             * *                
       1588 AGTTATAGGCGAAGGTCAAGGTCCATGTCAAGATCACCAATC
          1 AGTTATAGAAGAAGGTCAAGGTCAAAGTCAAGATCACCAATC

              *     
       1630 AGCTATAG
          1 AGTTATAG

       1638 GCAAAGGAGG


Statistics
Matches: 42,  Mismatches: 7, Indels: 2
        0.82            0.14        0.04

Matches are distributed among these distances:
  41    1  0.02
  42   41  0.98

ACGTcount: A:0.36, C:0.21, G:0.22, T:0.22


Consensus pattern (42 bp):   
AGTTATAGAAGAAGGTCAAGGTCAAAGTCAAGATCACCAATC

Found at i:1638 original size:42 final size:42

Alignment explanation


    Indices: 1560--1644  Score: 125
    Period size: 42  Copynumber: 2.0  Consensus size: 42

       1550 ATCGAAGACA

                           *              *       *   
       1560 GTCAAGGTCAAAGTCTAGATCACCAATCAGTTATAGGCGAAG
          1 GTCAAGGTCAAAGTCAAGATCACCAATCAGCTATAGGCAAAG

                     * *                              
       1602 GTCAAGGTCCATGTCAAGATCACCAATCAGCTATAGGCAAAG
          1 GTCAAGGTCAAAGTCAAGATCACCAATCAGCTATAGGCAAAG

             
       1644 G
          1 G

       1645 AGGAGGTCTT


Statistics
Matches: 38,  Mismatches: 5, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  42   38  1.00

ACGTcount: A:0.35, C:0.21, G:0.24, T:0.20


Consensus pattern (42 bp):   
GTCAAGGTCAAAGTCAAGATCACCAATCAGCTATAGGCAAAG
Done.