Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_16787

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, 609

Length: 1016
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28


Found at i:544 original size:54 final size:54

Alignment explanation


    Indices: 462--587  Score: 236
    Period size: 54  Copynumber: 2.3  Consensus size: 54

        452 CTTATCACCA

                                                                   
        462 TGGTCC-AGTTGCAAAGCCACCCACAGGATCATCTCCGGTTCCTGCTCTGGCTCC
          1 TGGTCCTA-TTGCAAAGCCACCCACAGGATCATCTCCGGTTCCTGCTCTGGCTCC

                                                                  
        516 TGGTCCTATTGCAAAGCCACCCACAGGATCATCTCCGGTTCCTGCTCTGGCTCC
          1 TGGTCCTATTGCAAAGCCACCCACAGGATCATCTCCGGTTCCTGCTCTGGCTCC

                              
        570 TGGTCCTATTGCAAAGCC
          1 TGGTCCTATTGCAAAGCC

        588 TCCTACAGCA


Statistics
Matches: 71,  Mismatches: 0, Indels: 2
        0.97            0.00        0.03

Matches are distributed among these distances:
  54   70  0.99
  55    1  0.01

ACGTcount: A:0.17, C:0.36, G:0.21, T:0.25


Consensus pattern (54 bp):   
TGGTCCTATTGCAAAGCCACCCACAGGATCATCTCCGGTTCCTGCTCTGGCTCC

Found at i:624 original size:54 final size:54

Alignment explanation


    Indices: 462--624  Score: 168
    Period size: 54  Copynumber: 3.0  Consensus size: 54

        452 CTTATCACCA

                                       *    *          *  * *      
        462 TGGTCC-AGTTGCAAAGCCACCCACAGGATCATCTCCGGTTCCTGCTCTGGCTCC
          1 TGGTCCTA-TTGCAAAGCCACCCACAGCATCAACTCCGGTTCCAGCACAGGCTCC

                                      *    *          *  * *      
        516 TGGTCCTATTGCAAAGCCACCCACAGGATCATCTCCGGTTCCTGCTCTGGCTCC
          1 TGGTCCTATTGCAAAGCCACCCACAGCATCAACTCCGGTTCCAGCACAGGCTCC

                              *  *       *                    *    
        570 TGGTCCTATTGCAAAGCCTCCTACAGCATTAACTCCAGG-TCCAGCACAGTCTCC
          1 TGGTCCTATTGCAAAGCCACCCACAGCATCAACTCC-GGTTCCAGCACAGGCTCC

             
        624 T
          1 T

        625 TATCACCATG


Statistics
Matches: 98,  Mismatches: 9, Indels: 4
        0.88            0.08        0.04

Matches are distributed among these distances:
  54   95  0.97
  55    3  0.03

ACGTcount: A:0.19, C:0.36, G:0.20, T:0.25


Consensus pattern (54 bp):   
TGGTCCTATTGCAAAGCCACCCACAGCATCAACTCCGGTTCCAGCACAGGCTCC
Done.