Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_19186

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, 320

Length: 534
ACGTcount: A:0.31, C:0.15, G:0.33, T:0.20


Found at i:288 original size:24 final size:24

Alignment explanation


    Indices: 261--319  Score: 63
    Period size: 21  Copynumber: 2.6  Consensus size: 24

        251 ATGACAATGA

                                     
        261 TGATGAGGAAGATGAAGCA-GCAGG
          1 TGATGAGGAAGATGAAG-ATGCAGG

                   *                
        285 TGAT---CAAGATGAAGATGCAGG
          1 TGATGAGGAAGATGAAGATGCAGG

               *          
        306 TGAGGAGGAAGATG
          1 TGATGAGGAAGATG

        320 GATCAGGTGA


Statistics
Matches: 28,  Mismatches: 3, Indels: 8
        0.72            0.08        0.21

Matches are distributed among these distances:
  20    1  0.04
  21   17  0.61
  24   10  0.36

ACGTcount: A:0.37, C:0.07, G:0.41, T:0.15


Consensus pattern (24 bp):   
TGATGAGGAAGATGAAGATGCAGG

Found at i:293 original size:21 final size:21

Alignment explanation


    Indices: 269--308  Score: 64
    Period size: 21  Copynumber: 1.9  Consensus size: 21

        259 GATGATGAGG

                                  
        269 AAGATGAAGCA-GCAGGTGATC
          1 AAGATGAAG-ATGCAGGTGATC

                               
        290 AAGATGAAGATGCAGGTGA
          1 AAGATGAAGATGCAGGTGA

        309 GGAGGAAGAT


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  20    1  0.06
  21   17  0.94

ACGTcount: A:0.40, C:0.10, G:0.35, T:0.15


Consensus pattern (21 bp):   
AAGATGAAGATGCAGGTGATC

Found at i:475 original size:9 final size:9

Alignment explanation


    Indices: 463--503  Score: 64
    Period size: 9  Copynumber: 4.6  Consensus size: 9

        453 GGAAGGTGAA

                     
        463 GAAGAAGAG
          1 GAAGAAGAG

                     
        472 GAAGAAGAG
          1 GAAGAAGAG

                    *
        481 GAAGAAGAT
          1 GAAGAAGAG

              *      
        490 GAGGAAGAG
          1 GAAGAAGAG

                 
        499 GAAGA
          1 GAAGA

        504 GCTTCAGCCA


Statistics
Matches: 28,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
   9   28  1.00

ACGTcount: A:0.54, C:0.00, G:0.44, T:0.02


Consensus pattern (9 bp):   
GAAGAAGAG

Found at i:475 original size:12 final size:12

Alignment explanation


    Indices: 460--504  Score: 54
    Period size: 12  Copynumber: 3.8  Consensus size: 12

        450 CGAGGAAGGT

                    *  *
        460 GAAGAAGAAGAG
          1 GAAGAAGAGGAA

                        
        472 GAAGAAGAGGAA
          1 GAAGAAGAGGAA

                 *      
        484 GAAGATGAGGAA
          1 GAAGAAGAGGAA

              *      
        496 GAGGAAGAG
          1 GAAGAAGAG

        505 CTTCAGCCAC


Statistics
Matches: 28,  Mismatches: 5, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  12   28  1.00

ACGTcount: A:0.53, C:0.00, G:0.44, T:0.02


Consensus pattern (12 bp):   
GAAGAAGAGGAA

Done.