Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_29372

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, 262

Length: 438
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32


Found at i:166 original size:3 final size:3

Alignment explanation


    Indices: 160--209  Score: 57
    Period size: 3  Copynumber: 16.7  Consensus size: 3

        150 CACTCTTGCC

                                           *              *        *    
        160 TCT TCT TCT TCT TCT TCT TCT AT-A TCT TCT TCT TGT TCT TCA TCT
          1 TCT TCT TCT TCT TCT TCT TCT -TCT TCT TCT TCT TCT TCT TCT TCT

                  
        205 TCT TC
          1 TCT TC

        210 CTGTTCTTCC


Statistics
Matches: 39,  Mismatches: 6, Indels: 4
        0.80            0.12        0.08

Matches are distributed among these distances:
   2    1  0.03
   3   37  0.95
   4    1  0.03

ACGTcount: A:0.06, C:0.30, G:0.02, T:0.62


Consensus pattern (3 bp):   
TCT

Found at i:214 original size:18 final size:18

Alignment explanation


    Indices: 160--218  Score: 75
    Period size: 18  Copynumber: 3.3  Consensus size: 18

        150 CACTCTTGCC

                 *          * 
        160 TCTTCTTCTTCTTCTTCT
          1 TCTTCATCTTCTTCTTGT

                               
        178 TCTAT-ATCTTCTTCTTGT
          1 TCT-TCATCTTCTTCTTGT

                          *   
        196 TCTTCATCTTCTTCCTGT
          1 TCTTCATCTTCTTCTTGT

                 
        214 TCTTC
          1 TCTTC

        219 CTCTCCCTTT


Statistics
Matches: 36,  Mismatches: 3, Indels: 4
        0.84            0.07        0.09

Matches are distributed among these distances:
  17    1  0.03
  18   34  0.94
  19    1  0.03

ACGTcount: A:0.05, C:0.31, G:0.03, T:0.61


Consensus pattern (18 bp):   
TCTTCATCTTCTTCTTGT
Done.