Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_08404

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: 2542
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26


Found at i:240 original size:30 final size:30

Alignment explanation


    Indices: 204--333  Score: 163
    Period size: 30  Copynumber: 4.3  Consensus size: 30

        194 ATAACCCTGG

                         *       *        
        204 GTTGGTCAGCAACTCATCAGCTATCCCGGA
          1 GTTGGTCAGCAACACATCAGCAATCCCGGA

                               *      *  *
        234 GTTGGTCAGCAACACATCAACAATCCTGGT
          1 GTTGGTCAGCAACACATCAGCAATCCCGGA

                              *   *        
        264 GTTGGTCAGCAACTA-ATTAGCTATCCCGGA
          1 GTTGGTCAGCAAC-ACATCAGCAATCCCGGA

                                      *  *
        294 GTTGGTCAGCAACACATCAGCAATCCTGGT
          1 GTTGGTCAGCAACACATCAGCAATCCCGGA

                      
        324 GTTGGTCAGC
          1 GTTGGTCAGC

        334 TCATGGGTGT


Statistics
Matches: 84,  Mismatches: 14, Indels: 4
        0.82            0.14        0.04

Matches are distributed among these distances:
  29    1  0.01
  30   82  0.98
  31    1  0.01

ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25


Consensus pattern (30 bp):   
GTTGGTCAGCAACACATCAGCAATCCCGGA

Found at i:297 original size:60 final size:60

Alignment explanation


    Indices: 199--333  Score: 236
    Period size: 60  Copynumber: 2.3  Consensus size: 60

        189 CCTCAATAAC

                                *                                       
        199 CCTGG-GTTGGTCAGCAACTCATCAGCTATCCCGGAGTTGGTCAGCAACACATCAACAAT
          1 CCTGGTGTTGGTCAGCAACTAATCAGCTATCCCGGAGTTGGTCAGCAACACATCAACAAT

                                   *                               *    
        258 CCTGGTGTTGGTCAGCAACTAATTAGCTATCCCGGAGTTGGTCAGCAACACATCAGCAAT
          1 CCTGGTGTTGGTCAGCAACTAATCAGCTATCCCGGAGTTGGTCAGCAACACATCAACAAT

                            
        318 CCTGGTGTTGGTCAGC
          1 CCTGGTGTTGGTCAGC

        334 TCATGGGTGT


Statistics
Matches: 72,  Mismatches: 3, Indels: 1
        0.95            0.04        0.01

Matches are distributed among these distances:
  59    5  0.07
  60   67  0.93

ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24


Consensus pattern (60 bp):   
CCTGGTGTTGGTCAGCAACTAATCAGCTATCCCGGAGTTGGTCAGCAACACATCAACAAT
Done.