Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga05g01170.F2

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: 5334
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28


Found at i:407 original size:17 final size:17

Alignment explanation


    Indices: 385--419  Score: 61
    Period size: 17  Copynumber: 2.1  Consensus size: 17

        375 TCCTTCAATA

                        *    
        385 TTTGTTCCCCTATTTGG
          1 TTTGTTCCCCTAATTGG

                             
        402 TTTGTTCCCCTAATTGG
          1 TTTGTTCCCCTAATTGG

             
        419 T
          1 T

        420 AACTTTGCCC


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.09, C:0.23, G:0.17, T:0.51


Consensus pattern (17 bp):   
TTTGTTCCCCTAATTGG

Found at i:1103 original size:84 final size:84

Alignment explanation


    Indices: 909--1541  Score: 732
    Period size: 84  Copynumber: 7.6  Consensus size: 84

        899 AAGAAACAAG

                  *                                          *              *
        909 GAAGGCGGTTGAAGAAAGAAAATGTGCTGATTTGGAGATGGCTAAAGCAAAGGAGCAGAGGAAGT
          1 GAAGGCTGTTGAAGAAAGAAAATGTGCTGATTTGGAGATGGCTAAAGCACAGGAGCAGAGGAAGA

                       *   *     
        974 TTGTC-GAA-AAATCTAAG-A
         66 TTG-CAGAAGAGAT-GAAGAA

                   *       *               *                       *        *
        992 -AA-GCTTTTGAAGATAGAAAATGTGCTGATCTGGAGATGGCTAAAGCACAGGAGGAGAGGAAGG
          1 GAAGGCTGTTGAAGAAAGAAAATGTGCTGATTTGGAGATGGCTAAAGCACAGGAGCAGAGGAAGA

                               
       1055 TTGCAGAAGAGATGAAGAA
         66 TTGCAGAAGAGATGAAGAA

                                                   *                         
       1074 GAAGGCTGTTGAAGAAAGAAAATGTGCTGATTTGGAGATTGCTAAAGCACAGGAGC-GAAGGAAG
          1 GAAGGCTGTTGAAGAAAGAAAATGTGCTGATTTGGAGATGGCTAAAGCACAGGAGCAG-AGGAAG

             *                   
       1138 ACTGCAGAAGA-ATTGAAGAA
         65 ATTGCAGAAGAGA-TGAAGAA

                                                   *               *         
       1158 GAAGGCTGTTGAAGAAAGAAAATGTGCTGATTTGGAGATTGCTAAAGCACAGGAGAAGAGGAAGA
          1 GAAGGCTGTTGAAGAAAGAAAATGTGCTGATTTGGAGATGGCTAAAGCACAGGAGCAGAGGAAGA

            *                   
       1223 CTGCAGAAGA-ATTGAAGAA
         66 TTGCAGAAGAGA-TGAAGAA

                                   **     *                         *        
       1242 GAAGGCT-TCTGAAGAAAGAAAACATGCTGCTTTGGAGATGGCTAAAGCACAGGAGGAGAGGAAG
          1 GAAGGCTGT-TGAAGAAAGAAAATGTGCTGATTTGGAGATGGCTAAAGCACAGGAGCAGAGGAAG

                                 
       1306 ATTGCAGAAGAG-TCGAAGAA
         65 ATTGCAGAAGAGAT-GAAGAA

                                           *                             *   
       1326 GAAGGCTGTTGAAGAAAGAAAACATGTG--GCTTTGGAGATGGCTAAAGCACAGGAGCAGAAGAA
          1 GAAGGCTGTTGAAGAAAG-AAA-ATGTGCTGATTTGGAGATGGCTAAAGCACAGGAGCAGAGGAA

                           *     
       1389 GATTGCAGAAGAGATTAAGAA
         64 GATTGCAGAAGAGATGAAGAA

                  *         *     **         **        *     *   *   *  *    
       1410 GAAGGCAGTTGAAGAACGAAAACATGCTGATTTACAGATGGCTGAAGCAGAGGCGCAAAGAAAGA
          1 GAAGGCTGTTGAAGAAAGAAAATGTGCTGATTTGGAGATGGCTAAAGCACAGGAGCAGAGGAAGA

                      * **     
       1475 TTGCAGAAGAAACCAAGAA
         66 TTGCAGAAGAGATGAAGAA

                          *         *  *     *     *        
       1494 GAAGGCTGTTGAAGCAAGAAAATGGGCCGATTTTGAGATCGCTAAAGC
          1 GAAGGCTGTTGAAGAAAGAAAATGTGCTGATTTGGAGATGGCTAAAGC

       1542 GGAAGCGACT


Statistics
Matches: 478,  Mismatches: 55, Indels: 33
        0.84            0.10        0.06

Matches are distributed among these distances:
  80    1  0.00
  81   63  0.13
  82    9  0.02
  83    9  0.02
  84  387  0.81
  85    6  0.01
  86    3  0.01

ACGTcount: A:0.40, C:0.10, G:0.32, T:0.17


Consensus pattern (84 bp):   
GAAGGCTGTTGAAGAAAGAAAATGTGCTGATTTGGAGATGGCTAAAGCACAGGAGCAGAGGAAGA
TTGCAGAAGAGATGAAGAA

Done.