Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga04g01281.F1

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: 2852
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27


Found at i:298 original size:30 final size:30

Alignment explanation


    Indices: 262--391  Score: 163
    Period size: 30  Copynumber: 4.3  Consensus size: 30

        252 ATAACCCTGG

                         *       *        
        262 GTTGGTCAGCAACTCATCAGCTATCCCGGA
          1 GTTGGTCAGCAACACATCAGCAATCCCGGA

                               *      *  *
        292 GTTGGTCAGCAACACATCAACAATCCTGGT
          1 GTTGGTCAGCAACACATCAGCAATCCCGGA

                              *   *        
        322 GTTGGTCAGCAACTA-ATTAGCTATCCCGGA
          1 GTTGGTCAGCAAC-ACATCAGCAATCCCGGA

                                      *  *
        352 GTTGGTCAGCAACACATCAGCAATCCTGGT
          1 GTTGGTCAGCAACACATCAGCAATCCCGGA

                      
        382 GTTGGTCAGC
          1 GTTGGTCAGC

        392 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:355 original size:60 final size:60

Alignment explanation


    Indices: 257--391  Score: 236
    Period size: 60  Copynumber: 2.3  Consensus size: 60

        247 CCTCAATAAC

                                *                                       
        257 CCTGG-GTTGGTCAGCAACTCATCAGCTATCCCGGAGTTGGTCAGCAACACATCAACAAT
          1 CCTGGTGTTGGTCAGCAACTAATCAGCTATCCCGGAGTTGGTCAGCAACACATCAACAAT

                                   *                               *    
        316 CCTGGTGTTGGTCAGCAACTAATTAGCTATCCCGGAGTTGGTCAGCAACACATCAGCAAT
          1 CCTGGTGTTGGTCAGCAACTAATCAGCTATCCCGGAGTTGGTCAGCAACACATCAACAAT

                            
        376 CCTGGTGTTGGTCAGC
          1 CCTGGTGTTGGTCAGC

        392 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.