Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga08g01921.N1

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: 3127
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33


Found at i:86 original size:26 final size:26

Alignment explanation


    Indices: 49--158  Score: 166
    Period size: 26  Copynumber: 4.2  Consensus size: 26

         39 TGATACAAAT

                                      
         49 TGATAATAGGTTAGGTAAATGTTCCA
          1 TGATAATAGGTTAGGTAAATGTTCCA

                   *       *       *  
         75 TGATAATGGGTTAGGCAAATGTTTCA
          1 TGATAATAGGTTAGGTAAATGTTCCA

                                *     
        101 TGATAATAGGTTAGGTAAATATTCCA
          1 TGATAATAGGTTAGGTAAATGTTCCA

                   *               *  
        127 TGATAATGGGTTAGGTAAATGTTTCA
          1 TGATAATAGGTTAGGTAAATGTTCCA

                  
        153 TGATAA
          1 TGATAA

        159 GAATTTCATG


Statistics
Matches: 74,  Mismatches: 10, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  26   74  1.00

ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35


Consensus pattern (26 bp):   
TGATAATAGGTTAGGTAAATGTTCCA

Found at i:110 original size:52 final size:52

Alignment explanation


    Indices: 49--158  Score: 202
    Period size: 52  Copynumber: 2.1  Consensus size: 52

         39 TGATACAAAT

                                *                               
         49 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGCAAATGTTTCA
          1 TGATAATAGGTTAGGTAAATATTCCATGATAATGGGTTAGGCAAATGTTTCA

                                                     *          
        101 TGATAATAGGTTAGGTAAATATTCCATGATAATGGGTTAGGTAAATGTTTCA
          1 TGATAATAGGTTAGGTAAATATTCCATGATAATGGGTTAGGCAAATGTTTCA

                  
        153 TGATAA
          1 TGATAA

        159 GAATTTCATG


Statistics
Matches: 56,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  52   56  1.00

ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35


Consensus pattern (52 bp):   
TGATAATAGGTTAGGTAAATATTCCATGATAATGGGTTAGGCAAATGTTTCA

Found at i:1820 original size:27 final size:27

Alignment explanation


    Indices: 1782--1917  Score: 175
    Period size: 27  Copynumber: 5.0  Consensus size: 27

       1772 AAGCGTTCTA

                  *                    
       1782 GTGGCTATGCCACAAATATCTGATCTG
          1 GTGGCTCTGCCACAAATATCTGATCTG

                                       
       1809 GTGGCTCTGCCACAAATATCTGATCTG
          1 GTGGCTCTGCCACAAATATCTGATCTG

                          *       *    
       1836 GTGGCTCTGCCACATATATCTGTTCTG
          1 GTGGCTCTGCCACAAATATCTGATCTG

                         * *            
       1863 GTGGCTCTGCCACGATTATCTGTATCTG
          1 GTGGCTCTGCCACAAATATCTG-ATCTG

               *     *     *      *    
       1891 GTGACTCTGTCAC-ATTATCTGTTCTG
          1 GTGGCTCTGCCACAAATATCTGATCTG

             
       1917 G
          1 G

       1918 CAGCCATGCT


Statistics
Matches: 98,  Mismatches: 10, Indels: 3
        0.88            0.09        0.03

Matches are distributed among these distances:
  26    5  0.05
  27   78  0.80
  28   15  0.15

ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35


Consensus pattern (27 bp):   
GTGGCTCTGCCACAAATATCTGATCTG

Found at i:1864 original size:54 final size:55

Alignment explanation


    Indices: 1782--1917  Score: 195
    Period size: 54  Copynumber: 2.5  Consensus size: 55

       1772 AAGCGTTCTA

                  *       *       *                                
       1782 GTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACAAATATCTG-ATCTG
          1 GTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTATCTG

                                                    * *            
       1836 GTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACGATTATCTGTATCTG
          1 GTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTATCTG

               *     *                  
       1891 GTGACTCTGTCACAT-TATCTGTTCTGG
          1 GTGGCTCTGCCACATATATCTGTTCTGG

       1918 CAGCCATGCT


Statistics
Matches: 74,  Mismatches: 7, Indels: 2
        0.89            0.08        0.02

Matches are distributed among these distances:
  54   56  0.76
  55   18  0.24

ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35


Consensus pattern (55 bp):   
GTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTATCTG
Done.