Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga07g00013.F1

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: 4006
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36


Found at i:1706 original size:15 final size:15

Alignment explanation


    Indices: 1686--1714  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

       1676 TTATGCCCTT

                           
       1686 ACTATGCTTATTTCA
          1 ACTATGCTTATTTCA

                          
       1701 ACTATGCTTATTTC
          1 ACTATGCTTATTTC

       1715 TTTATCACTG


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.24, C:0.21, G:0.07, T:0.48


Consensus pattern (15 bp):   
ACTATGCTTATTTCA

Found at i:3956 original size:168 final size:166

Alignment explanation


    Indices: 3627--3957  Score: 380
    Period size: 168  Copynumber: 2.0  Consensus size: 166

       3617 TGTCTCACCT

                                *          *           *       *       *     
       3627 GTTTCTATGTCTTTATTCTTGCCACTTTGATCTTGGAAGAAGGGTAGTTAAGGAAAAGATAGTTT
          1 GTTTCTATGTCTTTATTCTTACCACTTTGATATTGGAAGAAGGCTAGTTAAAGAAAAGACAGTTT

                         *   *        *              *       *         *     
       3692 GGAGAGAGGCCTCTATAGCATGATTGTCTTTTTAGTAAAGTGAAATTTAGACCAAGATAGAGTAT
         66 GGAGAGAGGCCTCAATAACATGATTGGCTTTTTAGTAAAGTCAAATTTAAACCAAGATAAAGTAT

                **          *     * *           
       3757 GACTTGAATGTATTTCGATGTGGGGTTTGTAAACTA
        131 GACTCAAATGTATTTCAATGTGAGATTTGTAAACTA

                                 *  *                     *                  
       3793 GTTT-TATGTCTTTATTCTTATCATTTTGATATTGGAAGAAGGCTATTTACAAGAAAAGGACAGT
          1 GTTTCTATGTCTTTATTCTTACCACTTTGATATTGGAAGAAGGCTAGTTA-AAGAAAA-GACAGT

                  *                                  *    *         *   *    
       3857 TTGGAGTGAGGTCCT-AATAACATGATTGGCTTCTTTAGTAGAGTCTAATTTAAACTAAGTTAAA
         64 TTGGAGAGAGG-CCTCAATAACATGATTGGCTT-TTTAGTAAAGTCAAATTTAAACCAAGATAAA

                                                  
       3921 GTATGA-TCCAAATGTATTTCAATGTGAGATTTGTAAA
        127 GTATGACT-CAAATGTATTTCAATGTGAGATTTGTAAA

       3958 TTCGAAAAGT


Statistics
Matches: 136,  Mismatches: 24, Indels: 8
        0.81            0.14        0.05

Matches are distributed among these distances:
 165   39  0.29
 166   10  0.07
 167   30  0.22
 168   57  0.42

ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37


Consensus pattern (166 bp):   
GTTTCTATGTCTTTATTCTTACCACTTTGATATTGGAAGAAGGCTAGTTAAAGAAAAGACAGTTT
GGAGAGAGGCCTCAATAACATGATTGGCTTTTTAGTAAAGTCAAATTTAAACCAAGATAAAGTAT
GACTCAAATGTATTTCAATGTGAGATTTGTAAACTA
Done.