Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_15983

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, 336

Length: 561
ACGTcount: A:0.19, C:0.09, G:0.49, T:0.23


Found at i:109 original size:12 final size:12

Alignment explanation


    Indices: 82--128  Score: 64
    Period size: 12  Copynumber: 4.2  Consensus size: 12

         72 GTTAGGAAAG

                        
         82 GGAGGTGGT-G-
          1 GGAGGTGGTGGC

                        
         92 GG-GGTGGTGGC
          1 GGAGGTGGTGGC

                    *   
        103 GGAGGTGGAGGC
          1 GGAGGTGGTGGC

                        
        115 GGAGGTGGTGGC
          1 GGAGGTGGTGGC

              
        127 GG
          1 GG

        129 CTCTGGATCA


Statistics
Matches: 32,  Mismatches: 2, Indels: 4
        0.84            0.05        0.11

Matches are distributed among these distances:
   9    6  0.19
  10    3  0.09
  11    2  0.06
  12   21  0.66

ACGTcount: A:0.09, C:0.06, G:0.70, T:0.15


Consensus pattern (12 bp):   
GGAGGTGGTGGC

Found at i:280 original size:18 final size:18

Alignment explanation


    Indices: 230--292  Score: 72
    Period size: 18  Copynumber: 3.5  Consensus size: 18

        220 GGCAGTGGCA

                 *       *    
        230 ATGGAGGTGGGTCAGGAT
          1 ATGGAAGTGGGTCTGGAT

                ***   *       
        248 ATGGGTCTGGATCTGGAT
          1 ATGGAAGTGGGTCTGGAT

                              
        266 ATGGAAGTGGGTCTGGAT
          1 ATGGAAGTGGGTCTGGAT

                     
        284 ATGGAAGTG
          1 ATGGAAGTG

        293 AAGGCGGTAG


Statistics
Matches: 36,  Mismatches: 9, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
  18   36  1.00

ACGTcount: A:0.22, C:0.06, G:0.44, T:0.27


Consensus pattern (18 bp):   
ATGGAAGTGGGTCTGGAT

Found at i:460 original size:21 final size:21

Alignment explanation


    Indices: 436--482  Score: 60
    Period size: 21  Copynumber: 2.2  Consensus size: 21

        426 GAGTGGAAAT

                                  
        436 GGAGGTGGTAG-AGGTGGAGGA
          1 GGAGGTGGTAGCA-GTGGAGGA

                     *          *
        457 GGAGGTGGTGGCAGTGGAGGT
          1 GGAGGTGGTAGCAGTGGAGGA

                 
        478 GGAGG
          1 GGAGG

        483 AGGCGGAGGT


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  21   22  0.96
  22    1  0.04

ACGTcount: A:0.19, C:0.02, G:0.64, T:0.15


Consensus pattern (21 bp):   
GGAGGTGGTAGCAGTGGAGGA
Done.