Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_09473

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: 1905
ACGTcount: A:0.35, C:0.20, G:0.30, T:0.15


Found at i:458 original size:87 final size:87

Alignment explanation


    Indices: 355--532  Score: 338
    Period size: 87  Copynumber: 2.0  Consensus size: 87

        345 TGGGGCTGGA

                  *                                                          
        355 GCTGGAGCTGGACAGGAGAGAGGTACTTCAATGGCGTCTAAGGCCGAACACGAGAGTGATAAAGA
          1 GCTGGAACTGGACAGGAGAGAGGTACTTCAATGGCGTCTAAGGCCGAACACGAGAGTGATAAAGA

                                  
        420 GAAAGGACGACGGAGTTATGCT
         66 GAAAGGACGACGGAGTTATGCT

                                          *                                  
        442 GCTGGAACTGGACAGGAGAGAGGTACTTCAGTGGCGTCTAAGGCCGAACACGAGAGTGATAAAGA
          1 GCTGGAACTGGACAGGAGAGAGGTACTTCAATGGCGTCTAAGGCCGAACACGAGAGTGATAAAGA

                                  
        507 GAAAGGACGACGGAGTTATGCT
         66 GAAAGGACGACGGAGTTATGCT

                
        529 GCTG
          1 GCTG

        533 CTGCTGCTGG


Statistics
Matches: 89,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  87   89  1.00

ACGTcount: A:0.31, C:0.16, G:0.36, T:0.16


Consensus pattern (87 bp):   
GCTGGAACTGGACAGGAGAGAGGTACTTCAATGGCGTCTAAGGCCGAACACGAGAGTGATAAAGA
GAAAGGACGACGGAGTTATGCT

Found at i:612 original size:99 final size:96

Alignment explanation


    Indices: 438--614  Score: 230
    Period size: 96  Copynumber: 1.8  Consensus size: 96

        428 GACGGAGTTA

                         *    *               *   *   *      *    *          
        438 TGCTGCTGGAACTGGACAGGAGAGAGGTACTTCAGTGGCGTCTAAGGCCGAACACGAGAGTGATA
          1 TGCTGCTGGAACTCGACAAGAGAGAGGTACTTCAATGGAGTCCAAGGCCAAACAAGAGAGTGATA

                                           
        503 AAGAGAAAGGACGACGGAGTTATGCTGCTGC
         66 AAGAGAAAGGACGACGGAGTTATGCTGCTGC

                                         *                                   
        534 TGCTGCTGG-ACATCGACAAGAGAGAGGTGCTTCAATGGAGTCCAAGGGCAGCAAACAAGAGAGT
          1 TGCTGCTGGAAC-TCGACAAGAGAGAGGTACTTCAATGGAGTCCAA-GGC--CAAACAAGAGAGT

                     *       
        598 GATAAAGAGCAAGGACG
         62 GATAAAGAGAAAGGACG

        615 CCGCACTCAA


Statistics
Matches: 68,  Mismatches: 9, Indels: 5
        0.83            0.11        0.06

Matches are distributed among these distances:
  95    2  0.03
  96   36  0.53
  97    3  0.04
  99   27  0.40

ACGTcount: A:0.32, C:0.18, G:0.34, T:0.16


Consensus pattern (96 bp):   
TGCTGCTGGAACTCGACAAGAGAGAGGTACTTCAATGGAGTCCAAGGCCAAACAAGAGAGTGATA
AAGAGAAAGGACGACGGAGTTATGCTGCTGC
Done.