Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_05940

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, 673

Length: 1122
ACGTcount: A:0.28, C:0.22, G:0.29, T:0.21


Found at i:593 original size:54 final size:54

Alignment explanation


    Indices: 511--631  Score: 170
    Period size: 54  Copynumber: 2.2  Consensus size: 54

        501 CGGATCCGGC

                  * *                          *    *             
        511 CGGAGATCAGAATTTGAGCAGCCTCCGCCGCCCGAGTTTGGATCTGGGTATCGA
          1 CGGAGACCCGAATTTGAGCAGCCTCCGCCGCCCGAATTTGAATCTGGGTATCGA

                                         *  *                  * *
        565 CGGAGACCCGAATTTGAGCAGCCTCCGCCTCCTGAATTTGAATCTGGGTATGGC
          1 CGGAGACCCGAATTTGAGCAGCCTCCGCCGCCCGAATTTGAATCTGGGTATCGA

                         
        619 CGGAGACCCGAAT
          1 CGGAGACCCGAAT

        632 ATGGCGAACA


Statistics
Matches: 59,  Mismatches: 8, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  54   59  1.00

ACGTcount: A:0.21, C:0.27, G:0.30, T:0.21


Consensus pattern (54 bp):   
CGGAGACCCGAATTTGAGCAGCCTCCGCCGCCCGAATTTGAATCTGGGTATCGA

Found at i:947 original size:45 final size:45

Alignment explanation


    Indices: 883--1004  Score: 226
    Period size: 45  Copynumber: 2.7  Consensus size: 45

        873 CGGGTATGAG

                 *                                       
        883 AGGAAACCAAGTTATGGTAGATCCGAGGAAGAGGAAGAAGGATAT
          1 AGGAAGCCAAGTTATGGTAGATCCGAGGAAGAGGAAGAAGGATAT

                                         *               
        928 AGGAAGCCAAGTTATGGTAGATCCGAGGAGGAGGAAGAAGGATAT
          1 AGGAAGCCAAGTTATGGTAGATCCGAGGAAGAGGAAGAAGGATAT

                                            
        973 AGGAAGCCAAGTTATGGTAGATCCGAGGAAGA
          1 AGGAAGCCAAGTTATGGTAGATCCGAGGAAGA

       1005 AGGATATGGC


Statistics
Matches: 74,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  45   74  1.00

ACGTcount: A:0.39, C:0.10, G:0.35, T:0.16


Consensus pattern (45 bp):   
AGGAAGCCAAGTTATGGTAGATCCGAGGAAGAGGAAGAAGGATAT
Done.