Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga05g03050.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, 654

Length: 1090
ACGTcount: A:0.23, C:0.10, G:0.34, T:0.33


Found at i:366 original size:21 final size:21

Alignment explanation


    Indices: 342--391  Score: 64
    Period size: 21  Copynumber: 2.4  Consensus size: 21

        332 GTGTAGGAAA

                                 
        342 AGGAGGTGGTGGTGGAGGAGG
          1 AGGAGGTGGTGGTGGAGGAGG

                  **          *  
        363 AGGAGGAAGTGGTGGAGGTGG
          1 AGGAGGTGGTGGTGGAGGAGG

               *    
        384 AGGTGGTG
          1 AGGAGGTG

        392 CTAATGGTTT


Statistics
Matches: 23,  Mismatches: 6, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  21   23  1.00

ACGTcount: A:0.20, C:0.00, G:0.64, T:0.16


Consensus pattern (21 bp):   
AGGAGGTGGTGGTGGAGGAGG

Found at i:558 original size:12 final size:12

Alignment explanation


    Indices: 541--582  Score: 57
    Period size: 12  Copynumber: 3.5  Consensus size: 12

        531 AGGCCAAGGG

                        
        541 TATGGGTCTGGA
          1 TATGGGTCTGGA

                    *   
        553 TATGGGTCCGGA
          1 TATGGGTCTGGA

              *        *
        565 TACGGGTCTGGG
          1 TATGGGTCTGGA

                  
        577 TATGGG
          1 TATGGG

        583 AATGGTGTAG


Statistics
Matches: 25,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  12   25  1.00

ACGTcount: A:0.14, C:0.12, G:0.45, T:0.29


Consensus pattern (12 bp):   
TATGGGTCTGGA

Found at i:626 original size:30 final size:30

Alignment explanation


    Indices: 591--650  Score: 93
    Period size: 30  Copynumber: 2.0  Consensus size: 30

        581 GGAATGGTGT

                     *                    
        591 AGGAGGTGGTGGAGGCGGAGGTAGAGGAGG
          1 AGGAGGTGGCGGAGGCGGAGGTAGAGGAGG

                           *        *     
        621 AGGAGGTGGCGGAGGTGGAGGTAGTGGAGG
          1 AGGAGGTGGCGGAGGCGGAGGTAGAGGAGG

        651 TGGACATGGC


Statistics
Matches: 27,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  30   27  1.00

ACGTcount: A:0.22, C:0.03, G:0.63, T:0.12


Consensus pattern (30 bp):   
AGGAGGTGGCGGAGGCGGAGGTAGAGGAGG

Found at i:651 original size:15 final size:15

Alignment explanation


    Indices: 592--654  Score: 72
    Period size: 15  Copynumber: 4.2  Consensus size: 15

        582 GAATGGTGTA

                  *       *
        592 GGAGGTGGTGGAGGC
          1 GGAGGTAGTGGAGGT

                    *     *
        607 GGAGGTAGAGGAGGA
          1 GGAGGTAGTGGAGGT

                  * *      
        622 GGAGGTGGCGGAGGT
          1 GGAGGTAGTGGAGGT

                           
        637 GGAGGTAGTGGAGGT
          1 GGAGGTAGTGGAGGT

               
        652 GGA
          1 GGA

        655 CATGGCTCAG


Statistics
Matches: 40,  Mismatches: 8, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  15   40  1.00

ACGTcount: A:0.21, C:0.03, G:0.63, T:0.13


Consensus pattern (15 bp):   
GGAGGTAGTGGAGGT

Found at i:707 original size:6 final size:6

Alignment explanation


    Indices: 700--772  Score: 62
    Period size: 6  Copynumber: 12.7  Consensus size: 6

        690 ATACGGAAGC

                 *    *      *                                    *
        700 GGTGGC GGTAGA GGTAGA GGTGGA GGTGGA GGTGGA GGT--- GGTGGT
          1 GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA

                     *         *      *     
        745 GGTGGA GGAGGA GGTGGT GGTGGC GGTG
          1 GGTGGA GGTGGA GGTGGA GGTGGA GGTG

        773 ACAATGGTTA


Statistics
Matches: 56,  Mismatches: 8, Indels: 6
        0.80            0.11        0.09

Matches are distributed among these distances:
   3    3  0.05
   6   53  0.95

ACGTcount: A:0.14, C:0.03, G:0.64, T:0.19


Consensus pattern (6 bp):   
GGTGGA

Found at i:748 original size:21 final size:21

Alignment explanation


    Indices: 718--767  Score: 82
    Period size: 21  Copynumber: 2.4  Consensus size: 21

        708 TAGAGGTAGA

                 *        *      
        718 GGTGGAGGTGGAGGTGGAGGT
          1 GGTGGTGGTGGAGGAGGAGGT

                                 
        739 GGTGGTGGTGGAGGAGGAGGT
          1 GGTGGTGGTGGAGGAGGAGGT

                    
        760 GGTGGTGG
          1 GGTGGTGG

        768 CGGTGACAAT


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

Matches are distributed among these distances:
  21   27  1.00

ACGTcount: A:0.12, C:0.00, G:0.68, T:0.20


Consensus pattern (21 bp):   
GGTGGTGGTGGAGGAGGAGGT

Done.