Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_07112

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, 404

Length: 674
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.25


Found at i:250 original size:16 final size:16

Alignment explanation


    Indices: 229--268  Score: 57
    Period size: 15  Copynumber: 2.6  Consensus size: 16

        219 GTCCCACCAA

                            
        229 TACCAAACCCTCCCGT
          1 TACCAAACCCTCCCGT

                         *  
        245 TACC-AACCCTCCTGT
          1 TACCAAACCCTCCCGT

                      
        260 TA-CAAACCC
          1 TACCAAACCC

        269 ACCACCTTCT


Statistics
Matches: 22,  Mismatches: 1, Indels: 3
        0.85            0.04        0.12

Matches are distributed among these distances:
  14    1  0.05
  15   17  0.77
  16    4  0.18

ACGTcount: A:0.28, C:0.47, G:0.05, T:0.20


Consensus pattern (16 bp):   
TACCAAACCCTCCCGT

Found at i:330 original size:15 final size:15

Alignment explanation


    Indices: 306--352  Score: 58
    Period size: 15  Copynumber: 3.1  Consensus size: 15

        296 TGGTGGAGGG

                 *         
        306 GGAGGCGGCGGTGGA
          1 GGAGGTGGCGGTGGA

                          *
        321 GGAGGTGGCGGTGGC
          1 GGAGGTGGCGGTGGA

              *     *      
        336 GGTGGTGGAGGTGGA
          1 GGAGGTGGCGGTGGA

              
        351 GG
          1 GG

        353 TGGAGGTGGT


Statistics
Matches: 27,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  15   27  1.00

ACGTcount: A:0.11, C:0.09, G:0.68, T:0.13


Consensus pattern (15 bp):   
GGAGGTGGCGGTGGA

Found at i:336 original size:21 final size:21

Alignment explanation


    Indices: 296--376  Score: 99
    Period size: 21  Copynumber: 3.9  Consensus size: 21

        286 ACCCACCTTC

                     *     *     
        296 TGGTGGAGGGGGAGGCGGCGG
          1 TGGTGGAGGTGGAGGTGGCGG

               *        *        
        317 TGGAGGAGGTGGCGGTGGCGG
          1 TGGTGGAGGTGGAGGTGGCGG

                              *  
        338 TGGTGGAGGTGGAGGTGGAGG
          1 TGGTGGAGGTGGAGGTGGCGG

                  *     *     
        359 TGGTGGCGGTGGTGGTGG
          1 TGGTGGAGGTGGAGGTGG

        377 TGGGGGTAGC


Statistics
Matches: 51,  Mismatches: 9, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   51  1.00

ACGTcount: A:0.09, C:0.06, G:0.68, T:0.17


Consensus pattern (21 bp):   
TGGTGGAGGTGGAGGTGGCGG

Found at i:342 original size:9 final size:9

Alignment explanation


    Indices: 324--379  Score: 58
    Period size: 9  Copynumber: 6.2  Consensus size: 9

        314 CGGTGGAGGA

                 *   
        324 GGTGGCGGT
          1 GGTGGTGGT

              *      
        333 GGCGGTGGT
          1 GGTGGTGGT

              *     *
        342 GGAGGTGGA
          1 GGTGGTGGT

                 *   
        351 GGTGGAGGT
          1 GGTGGTGGT

                 *   
        360 GGTGGCGGT
          1 GGTGGTGGT

                     
        369 GGTGGTGGT
          1 GGTGGTGGT

              
        378 GG
          1 GG

        380 GGGTAGCACT


Statistics
Matches: 38,  Mismatches: 9, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
   9   38  1.00

ACGTcount: A:0.05, C:0.05, G:0.68, T:0.21


Consensus pattern (9 bp):   
GGTGGTGGT

Found at i:354 original size:15 final size:15

Alignment explanation


    Indices: 315--379  Score: 76
    Period size: 15  Copynumber: 4.3  Consensus size: 15

        305 GGGAGGCGGC

                    *     *
        315 GGTGGAGGAGGTGGC
          1 GGTGGAGGTGGTGGT

                 *        *
        330 GGTGGCGGTGGTGGA
          1 GGTGGAGGTGGTGGT

                       *   
        345 GGTGGAGGTGGAGGT
          1 GGTGGAGGTGGTGGT

                 *         
        360 GGTGGCGGTGGTGGT
          1 GGTGGAGGTGGTGGT

                 
        375 GGTGG
          1 GGTGG

        380 GGGTAGCACT


Statistics
Matches: 42,  Mismatches: 8, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  15   42  1.00

ACGTcount: A:0.08, C:0.05, G:0.68, T:0.20


Consensus pattern (15 bp):   
GGTGGAGGTGGTGGT

Found at i:372 original size:12 final size:12

Alignment explanation


    Indices: 318--376  Score: 55
    Period size: 12  Copynumber: 4.9  Consensus size: 12

        308 AGGCGGCGGT

                 *      
        318 GGAGGAGGTGGC
          1 GGAGGTGGTGGC

              *  *     *
        330 GGTGGCGGTGGT
          1 GGAGGTGGTGGC

                    *  *
        342 GGAGGTGGAGGT
          1 GGAGGTGGTGGC

                        
        354 GGAGGTGGTGGC
          1 GGAGGTGGTGGC

              *        
        366 GGTGGTGGTGG
          1 GGAGGTGGTGG

        377 TGGGGGTAGC


Statistics
Matches: 38,  Mismatches: 9, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  12   38  1.00

ACGTcount: A:0.08, C:0.05, G:0.68, T:0.19


Consensus pattern (12 bp):   
GGAGGTGGTGGC

Found at i:377 original size:6 final size:6

Alignment explanation


    Indices: 324--379  Score: 58
    Period size: 6  Copynumber: 9.3  Consensus size: 6

        314 CGGTGGAGGA

                 *      *          *      *      *         *       
        324 GGTGGC GGTGGC GGTGGT GGAGGT GGAGGT GGAGGT GGTGGC GGTGGT
          1 GGTGGT GGTGGT GGTGGT GGTGGT GGTGGT GGTGGT GGTGGT GGTGGT

                     
        372 GGTGGT GG
          1 GGTGGT GG

        380 GGGTAGCACT


Statistics
Matches: 45,  Mismatches: 5, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
   6   45  1.00

ACGTcount: A:0.05, C:0.05, G:0.68, T:0.21


Consensus pattern (6 bp):   
GGTGGT
Done.