Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga04g00168.F2

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, 799

Length: 1333
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.30


Found at i:158 original size:48 final size:48

Alignment explanation


    Indices: 106--376  Score: 314
    Period size: 48  Copynumber: 5.5  Consensus size: 48

         96 AACAGCGTTT

                                        *                   
        106 GCGTTTGCGTTTCTTTCGGAGGCGGAGGCGCCGGTGGTTGCATAAACA
          1 GCGTTTGCGTTTCTTTCGGAGGCGGAGGAGCCGGTGGTTGCATAAACA

                                                                  
        154 GCGTTTGCGTTTGCGTTTCTTTCGGAGGCGGAGGAGCCGGTGGTTGCATAAACA
          1 ------GCGTTTGCGTTTCTTTCGGAGGCGGAGGAGCCGGTGGTTGCATAAACA

                         *                    *  *          
        208 GCGTTTGCGTTTCCTTCGGAGGCGGAGGAGCCGGCGGCTGCATAAACA
          1 GCGTTTGCGTTTCTTTCGGAGGCGGAGGAGCCGGTGGTTGCATAAACA

            *   *        *  *              *  *             
        256 ACGTCTGCGTTTCCTTAGGAGGCGGAGGAGCAGGCGGTTGCATAAACA
          1 GCGTTTGCGTTTCTTTCGGAGGCGGAGGAGCCGGTGGTTGCATAAACA

                      *             *                          
        304 GCGTTTGCGTCTCTTTCGGAGGCGCA-GA--CGGTGGCTGTTGCATAAACA
          1 GCGTTTGCGTTTCTTTCGGAGGCGGAGGAGCCGGT-G--GTTGCATAAACA

                *     *              
        352 GCGTCTGCGTCTCTTTCGGAGGCGG
          1 GCGTTTGCGTTTCTTTCGGAGGCGG

        377 CGGCGGTTGC


Statistics
Matches: 195,  Mismatches: 19, Indels: 12
        0.86            0.08        0.05

Matches are distributed among these distances:
  45    2  0.01
  46    1  0.01
  47    2  0.01
  48  143  0.73
  54   47  0.24

ACGTcount: A:0.16, C:0.22, G:0.37, T:0.25


Consensus pattern (48 bp):   
GCGTTTGCGTTTCTTTCGGAGGCGGAGGAGCCGGTGGTTGCATAAACA

Found at i:171 original size:54 final size:54

Alignment explanation


    Indices: 83--313  Score: 297
    Period size: 54  Copynumber: 4.5  Consensus size: 54

         73 TTTCTTTTGG

                 *                                             *  
         83 CGGCGATTGCATAAACAGCGTTTGCGTTTGCGTTTCTTTCGGAGGCGGAGGCGC
          1 CGGCGGTTGCATAAACAGCGTTTGCGTTTGCGTTTCTTTCGGAGGCGGAGGAGC

               *                                                  
        137 CGGTGGTTGCATAAACAGCGTTTGCGTTTGCGTTTCTTTCGGAGGCGGAGGAGC
          1 CGGCGGTTGCATAAACAGCGTTTGCGTTTGCGTTTCTTTCGGAGGCGGAGGAGC

               *                                                  
        191 CGGTGGTTGCATAAACAGCGTTTGCGTTT-C----C-TTCGGAGGCGGAGGAGC
          1 CGGCGGTTGCATAAACAGCGTTTGCGTTTGCGTTTCTTTCGGAGGCGGAGGAGC

                  *          *                  *  *              
        239 CGGCGGCTGCATAAACAACG--T-C---TGCGTTTCCTTAGGAGGCGGAGGAGC
          1 CGGCGGTTGCATAAACAGCGTTTGCGTTTGCGTTTCTTTCGGAGGCGGAGGAGC

            *                          
        287 AGGCGGTTGCATAAACAGCGTTTGCGT
          1 CGGCGGTTGCATAAACAGCGTTTGCGT

        314 CTCTTTCGGA


Statistics
Matches: 156,  Mismatches: 10, Indels: 23
        0.83            0.05        0.12

Matches are distributed among these distances:
  42    1  0.01
  43    1  0.01
  45    1  0.01
  46    1  0.01
  47    1  0.01
  48   67  0.43
  49    1  0.01
  50    1  0.01
  51    1  0.01
  53    1  0.01
  54   80  0.51

ACGTcount: A:0.17, C:0.21, G:0.36, T:0.26


Consensus pattern (54 bp):   
CGGCGGTTGCATAAACAGCGTTTGCGTTTGCGTTTCTTTCGGAGGCGGAGGAGC

Done.