Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_13200

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, 835

Length: 1392
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.25


Found at i:169 original size:19 final size:20

Alignment explanation


    Indices: 142--180  Score: 53
    Period size: 19  Copynumber: 2.0  Consensus size: 20

        132 GGCAATGCTT

                                
        142 CCTTCTCATAATCATAATCA
          1 CCTTCTCATAATCATAATCA

                     *     *    
        162 CCTT-TCATCATCATCATCA
          1 CCTTCTCATAATCATAATCA

        181 TCATCATCAT


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

Matches are distributed among these distances:
  19   13  0.76
  20    4  0.24

ACGTcount: A:0.31, C:0.33, G:0.00, T:0.36


Consensus pattern (20 bp):   
CCTTCTCATAATCATAATCA

Found at i:174 original size:3 final size:3

Alignment explanation


    Indices: 166--191  Score: 52
    Period size: 3  Copynumber: 8.7  Consensus size: 3

        156 TAATCACCTT

                                              
        166 TCA TCA TCA TCA TCA TCA TCA TCA TC
          1 TCA TCA TCA TCA TCA TCA TCA TCA TC

        192 TTCTTCTTGT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   23  1.00

ACGTcount: A:0.31, C:0.35, G:0.00, T:0.35


Consensus pattern (3 bp):   
TCA

Done.