Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga02g00640.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, 1000

Length: 1942
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32


Found at i:167 original size:8 final size:8

Alignment explanation


    Indices: 154--190  Score: 65
    Period size: 8  Copynumber: 4.6  Consensus size: 8

        144 CTAGATTGGC

                    
        154 AAAAGCCG
          1 AAAAGCCG

                    
        162 AAAAGCCG
          1 AAAAGCCG

                    
        170 AAAAGCCG
          1 AAAAGCCG

               *    
        178 AAATGCCG
          1 AAAAGCCG

                 
        186 AAAAG
          1 AAAAG

        191 TCGGTATTTT


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   8   27  1.00

ACGTcount: A:0.51, C:0.22, G:0.24, T:0.03


Consensus pattern (8 bp):   
AAAAGCCG

Found at i:648 original size:27 final size:27

Alignment explanation


    Indices: 607--720  Score: 113
    Period size: 27  Copynumber: 4.2  Consensus size: 27

        597 GAGGAAGCGT

                      *                
        607 TCTGGTGGCTATGCCACAAATATCTGA
          1 TCTGGTGGCTCTGCCACAAATATCTGA

                *             *       *
        634 TCTGATGGCTCTGCCACATATATCTGT
          1 TCTGGTGGCTCTGCCACAAATATCTGA

                             * *      * 
        661 TCTGGTGGCTCTGCCACGATTATCTTTA
          1 TCTGGTGGCTCTGCCACAAATATC-TGA

                   *     *     *      *
        689 TCTGGTGACTCTGTCAC-ATTATCTGT
          1 TCTGGTGGCTCTGCCACAAATATCTGA

                  
        715 TCTGGT
          1 TCTGGT

        721 AGCCATGCTG


Statistics
Matches: 72,  Mismatches: 14, Indels: 3
        0.81            0.16        0.03

Matches are distributed among these distances:
  26    7  0.10
  27   49  0.68
  28   16  0.22

ACGTcount: A:0.18, C:0.24, G:0.21, T:0.38


Consensus pattern (27 bp):   
TCTGGTGGCTCTGCCACAAATATCTGA

Found at i:712 original size:54 final size:54

Alignment explanation


    Indices: 605--720  Score: 153
    Period size: 54  Copynumber: 2.1  Consensus size: 54

        595 TCGAGGAAGC

                                                *                 
        605 GTTCTGGTGGCTATGCCACAAATATCTGATCTGATGGCTCTGCCACATATATCT
          1 GTTCTGGTGGCTATGCCACAAATATCTGATCTGATGACTCTGCCACATATATCT

                        *      * *      *     *        *           
        659 GTTCTGGTGGCTCTGCCACGATTATCTTTATCTGGTGACTCTGTCACAT-TATCT
          1 GTTCTGGTGGCTATGCCACAAATATC-TGATCTGATGACTCTGCCACATATATCT

                    
        713 GTTCTGGT
          1 GTTCTGGT

        721 AGCCATGCTG


Statistics
Matches: 54,  Mismatches: 7, Indels: 2
        0.86            0.11        0.03

Matches are distributed among these distances:
  54   36  0.67
  55   18  0.33

ACGTcount: A:0.17, C:0.23, G:0.22, T:0.38


Consensus pattern (54 bp):   
GTTCTGGTGGCTATGCCACAAATATCTGATCTGATGACTCTGCCACATATATCT

Found at i:805 original size:19 final size:22

Alignment explanation


    Indices: 781--820  Score: 59
    Period size: 19  Copynumber: 2.0  Consensus size: 22

        771 CTCCCCACAC

                                  
        781 GGTGTA-A-GGTTGG-TATGGG
          1 GGTGTATACGGTTGGATATGGG

                                 
        800 GGTGTATACGGTTGGATATGG
          1 GGTGTATACGGTTGGATATGG

        821 TTGGGTTTCT


Statistics
Matches: 18,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  19    6  0.33
  20    1  0.06
  21    6  0.33
  22    5  0.28

ACGTcount: A:0.17, C:0.03, G:0.47, T:0.33


Consensus pattern (22 bp):   
GGTGTATACGGTTGGATATGGG

Done.