Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_25724

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, 1000

Length: 1680
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.22


Found at i:355 original size:18 final size:18

Alignment explanation


    Indices: 334--408  Score: 71
    Period size: 18  Copynumber: 4.0  Consensus size: 18

        324 AAAAGATAGA

                    *  *      
        334 GAAAGGGATAGGGAGAGG
          1 GAAAGGGAGAGAGAGAGG

                                *
        352 GAAAAGGAGAGAGAGAGGAGA
          1 G-AAAGG-GAGAGAGA-GAGG

                             * 
        373 GAAAGGGAGA-AGGAGAAG
          1 GAAAGGGAGAGA-GAGAGG

                              
        391 GAAAGGGAGAGAGAGAGG
          1 GAAAGGGAGAGAGAGAGG

        409 AGAGAGAGGA


Statistics
Matches: 46,  Mismatches: 6, Indels: 10
        0.74            0.10        0.16

Matches are distributed among these distances:
  18   19  0.41
  19   12  0.26
  20   11  0.24
  21    4  0.09

ACGTcount: A:0.47, C:0.00, G:0.52, T:0.01


Consensus pattern (18 bp):   
GAAAGGGAGAGAGAGAGG

Found at i:372 original size:11 final size:11

Alignment explanation


    Indices: 356--416  Score: 60
    Period size: 11  Copynumber: 6.0  Consensus size: 11

        346 GAGAGGGAAA

                       
        356 AGGAGAGAGAG
          1 AGGAGAGAGAG

                    *  
        367 AGGAGAGAAAG
          1 AGGAGAGAGAG

                       
        378 -GGAGA-AG-G
          1 AGGAGAGAGAG

              *     *  
        386 AGAAG-GAAAG
          1 AGGAGAGAGAG

                       
        396 -GGAGAGAGAG
          1 AGGAGAGAGAG

                       
        406 AGGAGAGAGAG
          1 AGGAGAGAGAG

        417 GAGCAGCAGT


Statistics
Matches: 39,  Mismatches: 6, Indels: 10
        0.71            0.11        0.18

Matches are distributed among these distances:
   8    1  0.03
   9    8  0.21
  10   10  0.26
  11   20  0.51

ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00


Consensus pattern (11 bp):   
AGGAGAGAGAG

Found at i:380 original size:39 final size:39

Alignment explanation


    Indices: 331--413  Score: 130
    Period size: 39  Copynumber: 2.1  Consensus size: 39

        321 GGAAAAAGAT

                       * *     *                   
        331 AGAGAAAGGGATAGGGAGAGGGAAAAGGAGAGAGAGAGG
          1 AGAGAAAGGGAGAAGGAGAAGGAAAAGGAGAGAGAGAGG

                                     *             
        370 AGAGAAAGGGAGAAGGAGAAGGAAAGGGAGAGAGAGAGG
          1 AGAGAAAGGGAGAAGGAGAAGGAAAAGGAGAGAGAGAGG

                 
        409 AGAGA
          1 AGAGA

        414 GAGGAGCAGC


Statistics
Matches: 40,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  39   40  1.00

ACGTcount: A:0.48, C:0.00, G:0.51, T:0.01


Consensus pattern (39 bp):   
AGAGAAAGGGAGAAGGAGAAGGAAAAGGAGAGAGAGAGG

Found at i:392 original size:33 final size:34

Alignment explanation


    Indices: 315--407  Score: 89
    Period size: 33  Copynumber: 2.7  Consensus size: 34

        305 GTAGAGGAAG

                           *     *  *  *       *
        315 GGAAAAGGAAAAAGATAGAGAAAGGGATAGGGAGAG
          1 GGAAAAGG--AAAGAGAGAGAGAGAGAAAGGGAGAA

                     *                        
        351 GGAAAAGGAGAGAGAGAG-GAGAGAAAGGGAGAA
          1 GGAAAAGGAAAGAGAGAGAGAGAGAAAGGGAGAA

               *        *           
        384 GGAGAAGGAAAGGGAGAGAGAGAG
          1 GGAAAAGGAAAGAGAGAGAGAGAG

        408 GAGAGAGAGG


Statistics
Matches: 47,  Mismatches: 9, Indels: 4
        0.78            0.15        0.07

Matches are distributed among these distances:
  33   26  0.55
  34   13  0.28
  36    8  0.17

ACGTcount: A:0.51, C:0.00, G:0.47, T:0.02


Consensus pattern (34 bp):   
GGAAAAGGAAAGAGAGAGAGAGAGAAAGGGAGAA
Done.