Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g00159.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, 1000

Length: 2437
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30


Found at i:208 original size:50 final size:50

Alignment explanation


    Indices: 150--253  Score: 208
    Period size: 50  Copynumber: 2.1  Consensus size: 50

        140 TATGGAAACA

                                                              
        150 TAGGGAACCACTCAGTCGATTCGATCAAGAAAGTGGCAAAAACCAGATTC
          1 TAGGGAACCACTCAGTCGATTCGATCAAGAAAGTGGCAAAAACCAGATTC

                                                              
        200 TAGGGAACCACTCAGTCGATTCGATCAAGAAAGTGGCAAAAACCAGATTC
          1 TAGGGAACCACTCAGTCGATTCGATCAAGAAAGTGGCAAAAACCAGATTC

                
        250 TAGG
          1 TAGG

        254 AGAAAATGTC


Statistics
Matches: 54,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  50   54  1.00

ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18


Consensus pattern (50 bp):   
TAGGGAACCACTCAGTCGATTCGATCAAGAAAGTGGCAAAAACCAGATTC

Found at i:918 original size:225 final size:225

Alignment explanation


    Indices: 527--978  Score: 708
    Period size: 225  Copynumber: 2.0  Consensus size: 225

        517 CAGTCCTCGG

                                       *             *          *  *     *   
        527 TTAAGCCAGTTCTATATCCTCCTAGTCTGCTGCCATCATTTGAAACATCATTTACGGCCCAGAAA
          1 TTAAGCCAGTTCTATATCCTCCTAGTCCGCTGCCATCATTTAAAACATCATTCACAGCCCAAAAA

                                 *                              *            
        592 CCATCTCCATCACCTAAAGGATTGACACCACCTAAACCAACCACACCGTCTCTGAAACCCTCTTC
         66 CCATCTCCATCACCTAAAGGACTGACACCACCTAAACCAACCACACCGTCTCCGAAACCCTCTTC

                    *                                                        
        657 ATCGTCTTTTAAGCCAAGTCCATCCCTTAAGCCAACTCTATCAGAACTAGGGAAAGGAAAGTACA
        131 ATCGTCTTCTAAGCCAAGTCCATCCCTTAAGCCAACTCTATCAGAACTAGGGAAAGGAAAGTACA

                          *               
        722 AAACACTCAATCCAGAGGATACATTACCGA
        196 AAACACTCAATCCAAAGGATACATTACCGA

                                            *             **            *    
        752 TTAAGCC-GATTCTATATCCTCCTAGTCCGCTTCCATCATTTAAAATGTCATTCACAGCCGAAAA
          1 TTAAGCCAG-TTCTATATCCTCCTAGTCCGCTGCCATCATTTAAAACATCATTCACAGCCCAAAA

                                                 *                     *     
        816 ACCATCTCCATCACCTAAAGGACTGACACCACCTAAATCAACCACACCGTCTCCGAAACGCTCTT
         65 ACCATCTCCATCACCTAAAGGACTGACACCACCTAAACCAACCACACCGTCTCCGAAACCCTCTT

                                                       *                     
        881 CATCGTCTTCTAAGCCAAGTCCATCCCTTAAGCCAACTCTATCGGAACTAGGGAAAGGAAAGTAC
        130 CATCGTCTTCTAAGCCAAGTCCATCCCTTAAGCCAACTCTATCAGAACTAGGGAAAGGAAAGTAC

                  *  *            **       
        946 AAAACAGTCGATCCAAAGGATATGTTACCGA
        195 AAAACACTCAATCCAAAGGATACATTACCGA

              
        977 TT
          1 TT

        979 TACATGATTC


Statistics
Matches: 206,  Mismatches: 20, Indels: 2
        0.90            0.09        0.01

Matches are distributed among these distances:
 224    1  0.00
 225  205  1.00

ACGTcount: A:0.33, C:0.30, G:0.13, T:0.24


Consensus pattern (225 bp):   
TTAAGCCAGTTCTATATCCTCCTAGTCCGCTGCCATCATTTAAAACATCATTCACAGCCCAAAAA
CCATCTCCATCACCTAAAGGACTGACACCACCTAAACCAACCACACCGTCTCCGAAACCCTCTTC
ATCGTCTTCTAAGCCAAGTCCATCCCTTAAGCCAACTCTATCAGAACTAGGGAAAGGAAAGTACA
AAACACTCAATCCAAAGGATACATTACCGA
Done.