Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g00830.N2

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, 342

Length: 570
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33


Found at i:306 original size:36 final size:39

Alignment explanation


    Indices: 258--348  Score: 100
    Period size: 36  Copynumber: 2.3  Consensus size: 39

        248 CGTCGGCCGA

                   *       *                        
        258 GGTTTGGGGGTGGA-TTAGGAGGA-GG-AGGTGGTGGAG-
          1 GGTTTGGTGGTGGAGGT-GGAGGAGGGCAGGTGGTGGAGC

                                                    
        294 GGTTTGGTGGTGGAGGTGGAGGAGGGCTAGGTGGTGGAGC
          1 GGTTTGGTGGTGGAGGTGGAGGAGGGC-AGGTGGTGGAGC

                           
        334 TGGATTTGGTGGTGG
          1 -GG-TTTGGTGGTGG

        349 GTTCGGTGGT


Statistics
Matches: 46,  Mismatches: 2, Indels: 8
        0.82            0.04        0.14

Matches are distributed among these distances:
  36   19  0.41
  37    3  0.07
  39   11  0.24
  41    2  0.04
  42   11  0.24

ACGTcount: A:0.13, C:0.02, G:0.59, T:0.25


Consensus pattern (39 bp):   
GGTTTGGTGGTGGAGGTGGAGGAGGGCAGGTGGTGGAGC

Found at i:310 original size:24 final size:24

Alignment explanation


    Indices: 281--337  Score: 78
    Period size: 24  Copynumber: 2.4  Consensus size: 24

        271 ATTAGGAGGA

                    *      * *      
        281 GGAGGTGGTGGAGGGTTTGGTGGT
          1 GGAGGTGGAGGAGGGCTAGGTGGT

                                    
        305 GGAGGTGGAGGAGGGCTAGGTGGT
          1 GGAGGTGGAGGAGGGCTAGGTGGT

                *    
        329 GGAGCTGGA
          1 GGAGGTGGA

        338 TTTGGTGGTG


Statistics
Matches: 29,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  24   29  1.00

ACGTcount: A:0.14, C:0.04, G:0.61, T:0.21


Consensus pattern (24 bp):   
GGAGGTGGAGGAGGGCTAGGTGGT

Found at i:379 original size:30 final size:30

Alignment explanation


    Indices: 323--379  Score: 71
    Period size: 30  Copynumber: 1.9  Consensus size: 30

        313 AGGAGGGCTA

                            **   *        
        323 GGTGGTGGAGCTGGATTTGGTGGTGGGTTC
          1 GGTGGTGGAGCTGGATCAGGTAGTGGGTTC

                                        
        353 GGTGGTGGAGCTGG-TGCAGGTAGTGGG
          1 GGTGGTGGAGCTGGAT-CAGGTAGTGGG

        380 CTTGGAGGAG


Statistics
Matches: 23,  Mismatches: 3, Indels: 2
        0.82            0.11        0.07

Matches are distributed among these distances:
  29    1  0.04
  30   22  0.96

ACGTcount: A:0.09, C:0.07, G:0.56, T:0.28


Consensus pattern (30 bp):   
GGTGGTGGAGCTGGATCAGGTAGTGGGTTC
Done.