Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga05g03619.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: 2235
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33


Found at i:196 original size:16 final size:15

Alignment explanation


    Indices: 170--199  Score: 51
    Period size: 16  Copynumber: 1.9  Consensus size: 15

        160 ACTAGATTGG

                           
        170 CAAAAGCCGAAAAGC
          1 CAAAAGCCGAAAAGC

                           
        185 CAAAATGCCGAAAAG
          1 CAAAA-GCCGAAAAG

        200 TCGGTATTTT


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    5  0.36
  16    9  0.64

ACGTcount: A:0.53, C:0.23, G:0.20, T:0.03


Consensus pattern (15 bp):   
CAAAAGCCGAAAAGC

Found at i:656 original size:27 final size:27

Alignment explanation


    Indices: 615--729  Score: 167
    Period size: 27  Copynumber: 4.2  Consensus size: 27

        605 GAGGAAGCGT

                      *                
        615 TCTGGTGGCTATGCCACAAATATCTGA
          1 TCTGGTGGCTCTGCCACAAATATCTGA

                                       
        642 TCTGGTGGCTCTGCCACAAATATCTGA
          1 TCTGGTGGCTCTGCCACAAATATCTGA

                              *       *
        669 TCTGGTGGCTCTGCCACATATATCTGT
          1 TCTGGTGGCTCTGCCACAAATATCTGA

                     *       * *        
        696 TCTGGTGGCCCTGCCACGATTATCTGTA
          1 TCTGGTGGCTCTGCCACAAATATCTG-A

                  
        724 TCTGGT
          1 TCTGGT

        730 AACTCTGTCA


Statistics
Matches: 79,  Mismatches: 8, Indels: 1
        0.90            0.09        0.01

Matches are distributed among these distances:
  27   73  0.92
  28    6  0.08

ACGTcount: A:0.18, C:0.25, G:0.23, T:0.33


Consensus pattern (27 bp):   
TCTGGTGGCTCTGCCACAAATATCTGA

Found at i:700 original size:54 final size:55

Alignment explanation


    Indices: 615--754  Score: 185
    Period size: 54  Copynumber: 2.6  Consensus size: 55

        605 GAGGAAGCGT

                      *       *       *         *                  
        615 TCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACAAATATCTG-A
          1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCCCTGCCACAAATATCTGTA

                                                        * *        
        669 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCCCTGCCACGATTATCTGTA
          1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCCCTGCCACAAATATCTGTA

                  **     *                  
        724 TCTGGTAACTCTGTCACAT-TATCTGTTCTGG
          1 TCTGGTGGCTCTGCCACATATATCTGTTCTGG

        755 CAGCCATGCT


Statistics
Matches: 76,  Mismatches: 9, Indels: 2
        0.87            0.10        0.02

Matches are distributed among these distances:
  54   59  0.78
  55   17  0.22

ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34


Consensus pattern (55 bp):   
TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCCCTGCCACAAATATCTGTA

Found at i:744 original size:27 final size:28

Alignment explanation


    Indices: 615--754  Score: 157
    Period size: 27  Copynumber: 5.2  Consensus size: 28

        605 GAGGAAGCGT

                      *        *        
        615 TCTGGTGGCTATGCCACAAATATCTG-A
          1 TCTGGTGGCTCTGCCACAATTATCTGTA

                               *        
        642 TCTGGTGGCTCTGCCACAAATATCTG-A
          1 TCTGGTGGCTCTGCCACAATTATCTGTA

                                         
        669 TCTGGTGGCTCTGCCAC-ATATATCTGT-
          1 TCTGGTGGCTCTGCCACAAT-TATCTGTA

                     *       *          
        696 TCTGGTGGCCCTGCCACGATTATCTGTA
          1 TCTGGTGGCTCTGCCACAATTATCTGTA

                  **     *              
        724 TCTGGTAACTCTGTCAC-ATTATCTGT-
          1 TCTGGTGGCTCTGCCACAATTATCTGTA

                 
        750 TCTGG
          1 TCTGG

        755 CAGCCATGCT


Statistics
Matches: 102,  Mismatches: 7, Indels: 9
        0.86            0.06        0.08

Matches are distributed among these distances:
  26    6  0.06
  27   81  0.79
  28   15  0.15

ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34


Consensus pattern (28 bp):   
TCTGGTGGCTCTGCCACAATTATCTGTA
Done.