Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_01203

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, 318

Length: 531
ACGTcount: A:0.32, C:0.16, G:0.32, T:0.19


Found at i:308 original size:21 final size:21

Alignment explanation


    Indices: 283--337  Score: 58
    Period size: 21  Copynumber: 2.6  Consensus size: 21

        273 GGATGATGAG

                                * 
        283 GATGAGGAAGATGAAGCA-GGA
          1 GATGAGGAAGATGAAG-ATGCA

                 **              
        304 GATGATCAAGATGAAGATGCA
          1 GATGAGGAAGATGAAGATGCA

                    *    
        325 GATGAGGAGGATG
          1 GATGAGGAAGATG

        338 CATCTGGTGA


Statistics
Matches: 27,  Mismatches: 6, Indels: 2
        0.77            0.17        0.06

Matches are distributed among these distances:
  20    1  0.04
  21   26  0.96

ACGTcount: A:0.40, C:0.05, G:0.40, T:0.15


Consensus pattern (21 bp):   
GATGAGGAAGATGAAGATGCA

Found at i:423 original size:15 final size:15

Alignment explanation


    Indices: 403--431  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

        393 TGCCAGTGGA

                           
        403 GACGAGGATGATGAG
          1 GACGAGGATGATGAG

                          
        418 GACGAGGATGATGA
          1 GACGAGGATGATGA

        432 CGATGACGAC


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.34, C:0.07, G:0.45, T:0.14


Consensus pattern (15 bp):   
GACGAGGATGATGAG

Found at i:468 original size:9 final size:9

Alignment explanation


    Indices: 457--503  Score: 58
    Period size: 9  Copynumber: 5.2  Consensus size: 9

        447 TGATGGTGAG

                    *
        457 GAAGAGGAG
          1 GAAGAGGAA

                 *   
        466 GAAGAAGAA
          1 GAAGAGGAA

                     
        475 GAAGAGGAA
          1 GAAGAGGAA

              *     *
        484 GACGAGGAT
          1 GAAGAGGAA

                     
        493 GAAGAGGAA
          1 GAAGAGGAA

              
        502 GA
          1 GA

        504 GCTTCAGCCA


Statistics
Matches: 31,  Mismatches: 7, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
   9   31  1.00

ACGTcount: A:0.51, C:0.02, G:0.45, T:0.02


Consensus pattern (9 bp):   
GAAGAGGAA

Found at i:490 original size:24 final size:24

Alignment explanation


    Indices: 454--504  Score: 75
    Period size: 24  Copynumber: 2.1  Consensus size: 24

        444 CGATGATGGT

                    *               
        454 GAGGAAGAGGAGGAAGAAGAAGAA
          1 GAGGAAGACGAGGAAGAAGAAGAA

                          *     *   
        478 GAGGAAGACGAGGATGAAGAGGAA
          1 GAGGAAGACGAGGAAGAAGAAGAA

               
        502 GAG
          1 GAG

        505 CTTCAGCCAC


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.49, C:0.02, G:0.47, T:0.02


Consensus pattern (24 bp):   
GAGGAAGACGAGGAAGAAGAAGAA
Done.