Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_33782

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, 648

Length: 1080
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28


Found at i:158 original size:6 final size:6

Alignment explanation


    Indices: 91--137  Score: 94
    Period size: 6  Copynumber: 7.8  Consensus size: 6

         81 GAAAAGTGCT

                                                                  
         91 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTC
          1 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTC

        138 TTCCTATTCC


Statistics
Matches: 41,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   41  1.00

ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51


Consensus pattern (6 bp):   
TCTTCC

Found at i:166 original size:21 final size:21

Alignment explanation


    Indices: 115--180  Score: 71
    Period size: 21  Copynumber: 3.1  Consensus size: 21

        105 TTCCTCTTCC

                   *    *     *  
        115 TCTTCCTCTTCCTCTTCCTCT
          1 TCTTCCTATTCCCCTTCCCCT

                                 
        136 TCTTCCTATTCCCCTTCCCCT
          1 TCTTCCTATTCCCCTTCCCCT

                 *            *   
        157 TCTTCTTATTCTCCC-TCTCCT
          1 TCTTCCTATTC-CCCTTCCCCT

               
        178 TCT
          1 TCT

        181 CCTTCTCCTT


Statistics
Matches: 39,  Mismatches: 5, Indels: 2
        0.85            0.11        0.04

Matches are distributed among these distances:
  21   36  0.92
  22    3  0.08

ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50


Consensus pattern (21 bp):   
TCTTCCTATTCCCCTTCCCCT

Found at i:175 original size:6 final size:6

Alignment explanation


    Indices: 165--203  Score: 60
    Period size: 6  Copynumber: 6.5  Consensus size: 6

        155 CTTCTTCTTA

                   *                               *     
        165 TTCTCC CTCTCC TTCTCC TTCTCC TTCTCC TTCTAC TTC
          1 TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTC

        204 ATATCTCTCT


Statistics
Matches: 30,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
   6   30  1.00

ACGTcount: A:0.03, C:0.49, G:0.00, T:0.49


Consensus pattern (6 bp):   
TTCTCC

Done.