Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga10g01528.N4

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: 3948
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30


Found at i:3885 original size:16 final size:16

Alignment explanation


    Indices: 3862--3901  Score: 53
    Period size: 16  Copynumber: 2.5  Consensus size: 16

       3852 CGTTTGGTTC

                    *     * 
       3862 GCTGTAATGGAATAGA
          1 GCTGTAATAGAATAAA

             *              
       3878 GTTGTAATAGAATAAA
          1 GCTGTAATAGAATAAA

                    
       3894 GCTGTAAT
          1 GCTGTAAT

       3902 CAATAATTCA


Statistics
Matches: 20,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  16   20  1.00

ACGTcount: A:0.40, C:0.05, G:0.25, T:0.30


Consensus pattern (16 bp):   
GCTGTAATAGAATAAA

Found at i:3938 original size:118 final size:118

Alignment explanation


    Indices: 3729--3947  Score: 323
    Period size: 118  Copynumber: 1.9  Consensus size: 118

       3719 AAGGAAACAC

                                                            *        *     * 
       3729 TTGCACATATGGTTCGCTGTAATGGAATAGAGTTGTAAAGGAATAAAGTTATAATCAGTAATTTA
          1 TTGCACATATGGTTCGCTGTAATGGAATAGAGTTGTAAAGGAATAAAGCTATAATCAATAATTCA

               *   *        *    *       *                       
       3794 ATTGTTTGGTTGAATGGAATGGAATAGAATTGTAATGATATTCTTATGTTTGG
         66 ATTATTTAGTTGAATGAAATGAAATAGAACTGTAATGATATTCTTATGTTTGG

                  * *                                          *             
       3847 TTGCACGTTTGGTTCGCTGTAATGGAATAGAGTTGTAATA-GAATAAAGCTGTAATCAATAATTC
          1 TTGCACATATGGTTCGCTGTAATGGAATAGAGTTGTAA-AGGAATAAAGCTATAATCAATAATTC

                                                 
       3911 AATTATTTAGTTGAATGAAATGAAATAGAACTGTAAT
         65 AATTATTTAGTTGAATGAAATGAAATAGAACTGTAAT

       3948 T


Statistics
Matches: 89,  Mismatches: 11, Indels: 2
        0.87            0.11        0.02

Matches are distributed among these distances:
 118   88  0.99
 119    1  0.01

ACGTcount: A:0.35, C:0.06, G:0.22, T:0.37


Consensus pattern (118 bp):   
TTGCACATATGGTTCGCTGTAATGGAATAGAGTTGTAAAGGAATAAAGCTATAATCAATAATTCA
ATTATTTAGTTGAATGAAATGAAATAGAACTGTAATGATATTCTTATGTTTGG
Done.