Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_05316

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: 4404
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.30


Found at i:63 original size:15 final size:15

Alignment explanation


    Indices: 43--77  Score: 52
    Period size: 15  Copynumber: 2.3  Consensus size: 15

         33 TAGTTTACGG

                     *     
         43 GGAAGTTTACGAGCA
          1 GGAAGTTTAAGAGCA

                          *
         58 GGAAGTTTAAGAGCC
          1 GGAAGTTTAAGAGCA

                 
         73 GGAAG
          1 GGAAG

         78 CTCTTCGATA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  15   18  1.00

ACGTcount: A:0.34, C:0.11, G:0.37, T:0.17


Consensus pattern (15 bp):   
GGAAGTTTAAGAGCA

Found at i:1832 original size:20 final size:21

Alignment explanation


    Indices: 1803--1842  Score: 55
    Period size: 20  Copynumber: 2.0  Consensus size: 21

       1793 AAAGAGACCT

                 *       *       
       1803 CCTATTCTTT-CCTTCATGGG
          1 CCTATGCTTTACCATCATGGG

                                
       1823 CCTATGCTTTACCATCATGG
          1 CCTATGCTTTACCATCATGG

       1843 ATACTGAAGA


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  20    9  0.53
  21    8  0.47

ACGTcount: A:0.15, C:0.30, G:0.15, T:0.40


Consensus pattern (21 bp):   
CCTATGCTTTACCATCATGGG

Done.