Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_30980

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, 307

Length: 513
ACGTcount: A:0.24, C:0.25, G:0.28, T:0.23


Found at i:121 original size:15 final size:15

Alignment explanation


    Indices: 97--185  Score: 72
    Period size: 15  Copynumber: 5.7  Consensus size: 15

         87 TGGATCCTAC

                           
         97 CCTCCACAAGGATAT
          1 CCTCCACAAGGATAT

                 *         
        112 CCTCCTCAAGGATAT
          1 CCTCCACAAGGATAT

              *           *
        127 CCCCCACAAGGATAC
          1 CCTCCACAAGGATAT

              *   *  *      
        142 CCACCGGC-TGGATAT
          1 CCTCC-ACAAGGATAT

                       *      
        157 CCTCCACCAGCGGGATAT
          1 CCTCCA-CA--AGGATAT

                       
        175 CCTCCACAAGG
          1 CCTCCACAAGG

        186 CGGATACCCA


Statistics
Matches: 57,  Mismatches: 12, Indels: 10
        0.72            0.15        0.13

Matches are distributed among these distances:
  15   42  0.74
  16    1  0.02
  17    2  0.04
  18   12  0.21

ACGTcount: A:0.27, C:0.38, G:0.18, T:0.17


Consensus pattern (15 bp):   
CCTCCACAAGGATAT

Found at i:197 original size:33 final size:33

Alignment explanation


    Indices: 160--227  Score: 84
    Period size: 33  Copynumber: 2.1  Consensus size: 33

        150 TGGATATCCT

                                       *      
        160 CCACCAGC-GGGATATCCTCCACAAGGCGGATAC
          1 CCACCAGCAGGG-TATCCTCCACAAGGAGGATAC

                 *              *  *         
        193 CCACCTGCAGGGTATCCTCCTCATGGAGGATAC
          1 CCACCAGCAGGGTATCCTCCACAAGGAGGATAC

              
        226 CC
          1 CC

        228 TCATCCACCT


Statistics
Matches: 30,  Mismatches: 4, Indels: 2
        0.83            0.11        0.06

Matches are distributed among these distances:
  33   27  0.90
  34    3  0.10

ACGTcount: A:0.24, C:0.37, G:0.24, T:0.16


Consensus pattern (33 bp):   
CCACCAGCAGGGTATCCTCCACAAGGAGGATAC

Found at i:380 original size:21 final size:21

Alignment explanation


    Indices: 343--383  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        333 TCTTTACGGG

                                 
        343 GCTCACCATTTGTCACATGGA
          1 GCTCACCATTTGTCACATGGA

                 *               
        364 GCTCATCATCTTG-CACATGG
          1 GCTCACCAT-TTGTCACATGG

        384 GGGATACTAT


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  21   15  0.83
  22    3  0.17

ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29


Consensus pattern (21 bp):   
GCTCACCATTTGTCACATGGA

Found at i:429 original size:15 final size:15

Alignment explanation


    Indices: 403--444  Score: 57
    Period size: 15  Copynumber: 2.8  Consensus size: 15

        393 TGGCCATGGT

                 *         
        403 CACGGAAAATTTAAA
          1 CACGGGAAATTTAAA

              *           *
        418 CATGGGAAATTTAAG
          1 CACGGGAAATTTAAA

                        
        433 CACGGGAAATTT
          1 CACGGGAAATTT

        445 GGGAAGCGGT


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  15   23  1.00

ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24


Consensus pattern (15 bp):   
CACGGGAAATTTAAA
Done.