Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga05g03726.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: 12417
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32


Found at i:3287 original size:104 final size:105

Alignment explanation


    Indices: 3066--3314  Score: 303
    Period size: 105  Copynumber: 2.4  Consensus size: 105

       3056 TAAGTCTGAA

                          *       *                              *           
       3066 GCCGGCCATTGACAAGCCAGC-TCTAATTTTTTTTAAAATACTGGTACTCTGGTGCCATCCATTA
          1 GCCGGCCATTGACAGGCCAGCAACTAATTTTTTTTAAAATAC-GGTACTCTGGCGCCATCCATTA

                                           *         
       3130 ACAGACCAACACAAAAAAAATGATTTTTTTTTGTACTTGGT
         65 ACAGACCAACACAAAAAAAATGATTTTTTTTCGTACTTGGT

                                  * *                                *       
       3171 GCCGGCCATTGACAGGCCAGCACCAAATTTTTTTTTAAAATAC-GTACTCTGGCGTCGA-CCATT
          1 GCCGGCCATTGACAGGCCAGCAACTAA-TTTTTTTTAAAATACGGTACTCTGGCG-CCATCCATT

            *    *   *          * *                   
       3234 GACAGGCCAGCACAAAAAAATTTA-TTTTTTTCGTACTTGGT
         64 AACAGACCAACACAAAAAAAATGATTTTTTTTCGTACTTGGT

              **                                      
       3275 GCTTGCCATTGACAGGCCAG-AACTAA-TTTTTTTAAAATAC
          1 GCCGGCCATTGACAGGCCAGCAACTAATTTTTTTTAAAATAC

       3315 TAATATTTTT


Statistics
Matches: 126,  Mismatches: 15, Indels: 10
        0.83            0.10        0.07

Matches are distributed among these distances:
 101   14  0.11
 103    4  0.03
 104   34  0.27
 105   54  0.43
 106    5  0.04
 107   15  0.12

ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32


Consensus pattern (105 bp):   
GCCGGCCATTGACAGGCCAGCAACTAATTTTTTTTAAAATACGGTACTCTGGCGCCATCCATTAA
CAGACCAACACAAAAAAAATGATTTTTTTTCGTACTTGGT

Found at i:10780 original size:38 final size:38

Alignment explanation


    Indices: 10683--10785  Score: 152
    Period size: 38  Copynumber: 2.7  Consensus size: 38

      10673 GGCTTAAAGA

                                 **     *   *     
      10683 CCCGCAGGCTTCGTGCTGGTAAAATATCCGGGTTAAAT
          1 CCCGCAGGCTTCGTGCTGGTATTATATCAGGGATAAAT

                                                  
      10721 CCCGCAGGCTTCGTGCTGGTATTATATCAGGGATAAAT
          1 CCCGCAGGCTTCGTGCTGGTATTATATCAGGGATAAAT

                     * *               
      10759 CCCGCAGGCCTAGTGCTGGTATTATAT
          1 CCCGCAGGCTTCGTGCTGGTATTATAT

      10786 TCGGGCCTTC


Statistics
Matches: 59,  Mismatches: 6, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  38   59  1.00

ACGTcount: A:0.22, C:0.23, G:0.26, T:0.28


Consensus pattern (38 bp):   
CCCGCAGGCTTCGTGCTGGTATTATATCAGGGATAAAT

Found at i:11122 original size:43 final size:43

Alignment explanation


    Indices: 10783--11109  Score: 600
    Period size: 43  Copynumber: 7.6  Consensus size: 43

      10773 GCTGGTATTA

                                                       
      10783 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
          1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG

                                            *          
      10826 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGTCGGTGATGTG
          1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG

                                                       
      10869 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
          1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG

                                                       
      10912 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
          1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG

                                                      *
      10955 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTA
          1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG

                                         *             
      10998 TATTCGGGCCTTCGTGCCTAGCAGGCTTCTTGCCGGTGATGTG
          1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG

                * *                                    
      11041 TATTTGAGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
          1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG

                         *            
      11084 TATTCGGGCCTTCATGCCTAGCAGGC
          1 TATTCGGGCCTTCGTGCCTAGCAGGC

      11110 GTAATGCCGG


Statistics
Matches: 273,  Mismatches: 11, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  43  273  1.00

ACGTcount: A:0.10, C:0.25, G:0.33, T:0.31


Consensus pattern (43 bp):   
TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG

Done.