Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga06g01425.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, 386

Length: 644
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31


Found at i:338 original size:93 final size:92

Alignment explanation


    Indices: 179--350  Score: 240
    Period size: 93  Copynumber: 1.9  Consensus size: 92

        169 CTTGTGTGAA

                              *                   *                          
        179 CTAGTGTAAGACATGTCTGGGACATGCATCAGCCACATTACGAAGCCAGTGTAAGACCATGTCTG
          1 CTAGTGTAAGACATGTCTAGGACATGCATCAGCCACATGACGAAGCCAGTGTAAGACCATGTCTG

               *                        
        244 GGAGATGCCATCGGCAATGAGACAAGTG
         66 GGACATG-CATCGGCAATGAGACAAGTG

                                          *    *     *      *                
        272 CTAGTGTAAGACATGTCTAGGACATGCATCGGCCTCCA-GATGTAAGCTAGTGTAAGA-CATGTC
          1 CTAGTGTAAGACATGTCTAGGACATGCATCAGCC-ACATGACG-AAGCCAGTGTAAGACCATGTC

                            
        335 TGGGACATGCATCGGC
         64 TGGGACATGCATCGGC

        351 TAAAAGATGT


Statistics
Matches: 70,  Mismatches: 7, Indels: 5
        0.85            0.09        0.06

Matches are distributed among these distances:
  92    7  0.10
  93   48  0.69
  94   15  0.21

ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22


Consensus pattern (92 bp):   
CTAGTGTAAGACATGTCTAGGACATGCATCAGCCACATGACGAAGCCAGTGTAAGACCATGTCTG
GGACATGCATCGGCAATGAGACAAGTG

Found at i:349 original size:46 final size:43

Alignment explanation


    Indices: 179--350  Score: 173
    Period size: 46  Copynumber: 3.8  Consensus size: 43

        169 CTTGTGTGAA

                                          *   *   *      
        179 CTAGTGTAAGACATGTCTGGGACATGCATCAGCCACATTACGAAG
          1 CTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCA-GA-GAAG

             *                     *            * *   *     
        224 CCAGTGTAAGACCATGTCTGGGAGATGCCATCGGCAATGAGACAAGTG
          1 CTAGTGTAAGA-CATGTCTGGGACATG-CATCGGC-CTCAGAGAA--G

                              *                           
        272 CTAGTGTAAGACATGTCTAGGACATGCATCGGCCTCCAGATGTAAG
          1 CTAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CAGA-G-AAG

                                             
        318 CTAGTGTAAGACATGTCTGGGACATGCATCGGC
          1 CTAGTGTAAGACATGTCTGGGACATGCATCGGC

        351 TAAAAGATGT


Statistics
Matches: 104,  Mismatches: 15, Indels: 15
        0.78            0.11        0.11

Matches are distributed among these distances:
  45   11  0.11
  46   59  0.57
  47   20  0.19
  48   14  0.13

ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22


Consensus pattern (43 bp):   
CTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCAGAGAAG

Found at i:359 original size:46 final size:45

Alignment explanation


    Indices: 179--437  Score: 165
    Period size: 46  Copynumber: 5.6  Consensus size: 45

        169 CTTGTGTGAA

                                          *  *   ** *     
        179 CTAGTGTAAGACATGTCTGGGACATGCATCAGCCACATTACG-AAG
          1 CTAGTGTAAGACATGTCTGGGACATGCATCGGCTA-AAGATGTAAG

             *                     *              *     *     
        224 CCAGTGTAAGACCATGTCTGGGAGATGCCATCGGC-AATGA-GACAAGTG
          1 CTAGTGTAAGA-CATGTCTGGGACATG-CATCGGCTAAAGATG-TAA--G

                              *                **         
        272 CTAGTGTAAGACATGTCTAGGACATGCATCGGCCTCCAGATGTAAG
          1 CTAGTGTAAGACATGTCTGGGACATGCATCGG-CTAAAGATGTAAG

                                                          
        318 CTAGTGTAAGACATGTCTGGGACATGCATCGGCTAAAAGATGT--G
          1 CTAGTGTAAGACATGTCTGGGACATGCATCGGCT-AAAGATGTAAG

                * *                          *    *           
        362 -TCACTATAAGACCATGTCTGGGACATGGCATCAG-TATAGATGTACTAG
          1 CT-AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTAAAGATGTA--AG

                *                        
        410 AACTTGTGTAAGACCATGTCTGGG-CATG
          1 --CTAGTGTAAGA-CATGTCTGGGACATG

        438 GCGTCGATGT


Statistics
Matches: 173,  Mismatches: 21, Indels: 37
        0.75            0.09        0.16

Matches are distributed among these distances:
  43    1  0.01
  44   16  0.09
  45   30  0.17
  46   67  0.39
  47   20  0.12
  48   17  0.10
  49    4  0.02
  50   17  0.10
  51    1  0.01

ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24


Consensus pattern (45 bp):   
CTAGTGTAAGACATGTCTGGGACATGCATCGGCTAAAGATGTAAG
Done.