Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_36149

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, 520

Length: 868
ACGTcount: A:0.29, C:0.35, G:0.12, T:0.25


Found at i:373 original size:45 final size:45

Alignment explanation


    Indices: 252--358  Score: 187
    Period size: 45  Copynumber: 2.4  Consensus size: 45

        242 CCCGCAACGC

                                                         
        252 AACCACCTCCCTCTCCTACTGTGGCACCACCAGCACCTGCTAATA
          1 AACCACCTCCCTCTCCTACTGTGGCACCACCAGCACCTGCTAATA

                                            *     *   *  
        297 AACCACCTCCCTCTCCTACTGTGGCACCACCATCACCTTCTACTA
          1 AACCACCTCCCTCTCCTACTGTGGCACCACCAGCACCTGCTAATA

                             
        342 AACCACCTCCCTCTCCT
          1 AACCACCTCCCTCTCCT

        359 GCTATAAAAC


Statistics
Matches: 59,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  45   59  1.00

ACGTcount: A:0.22, C:0.48, G:0.07, T:0.22


Consensus pattern (45 bp):   
AACCACCTCCCTCTCCTACTGTGGCACCACCAGCACCTGCTAATA

Found at i:385 original size:45 final size:45

Alignment explanation


    Indices: 252--373  Score: 136
    Period size: 45  Copynumber: 2.7  Consensus size: 45

        242 CCCGCAACGC

                                * ***       *     *   *  
        252 AACCACCTCCCTCTCCTACTGTGGCACCACCAGCACCTGCTAATA
          1 AACCACCTCCCTCTCCTACTATAAAACCACCATCACCTTCTACTA

                                * ***                    
        297 AACCACCTCCCTCTCCTACTGTGGCACCACCATCACCTTCTACTA
          1 AACCACCTCCCTCTCCTACTATAAAACCACCATCACCTTCTACTA

                             *              
        342 AACCACCTCCCTCTCCTGCTATAAAACCACCA
          1 AACCACCTCCCTCTCCTACTATAAAACCACCA

        374 CCCTCTCCTA


Statistics
Matches: 69,  Mismatches: 8, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  45   69  1.00

ACGTcount: A:0.25, C:0.46, G:0.07, T:0.21


Consensus pattern (45 bp):   
AACCACCTCCCTCTCCTACTATAAAACCACCATCACCTTCTACTA

Found at i:394 original size:24 final size:24

Alignment explanation


    Indices: 296--399  Score: 74
    Period size: 24  Copynumber: 4.5  Consensus size: 24

        286 ACCTGCTAAT

                    *            *  
        296 AAACCACCTCCCTCTCCTACTGTG
          1 AAACCACCACCCTCTCCTACTCTG

            **                        
        320 GCACCACCATCACCT-T-CTA--CT-
          1 AAACCACCA-C-CCTCTCCTACTCTG

                    *         *  * *
        341 AAACCACCTCCCTCTCCTGCTATA
          1 AAACCACCACCCTCTCCTACTCTG

                                    
        365 AAACCACCACCCTCTCCTACTCTG
          1 AAACCACCACCCTCTCCTACTCTG

             *         
        389 ACACCACCACC
          1 AAACCACCACC

        400 ACCCTCGCCA


Statistics
Matches: 59,  Mismatches: 14, Indels: 14
        0.68            0.16        0.16

Matches are distributed among these distances:
  19    3  0.05
  20    2  0.03
  21    8  0.14
  22    1  0.02
  23    1  0.02
  24   39  0.66
  25    2  0.03
  26    3  0.05

ACGTcount: A:0.25, C:0.49, G:0.05, T:0.21


Consensus pattern (24 bp):   
AAACCACCACCCTCTCCTACTCTG
Done.