Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga05g02807.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: 5039
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40


Found at i:742 original size:57 final size:57

Alignment explanation


    Indices: 654--767  Score: 228
    Period size: 57  Copynumber: 2.0  Consensus size: 57

        644 ACTACAGTAA

                                                                     
        654 GGGAATGCGATGCTATTGATTATTATTAAGATTTCTCACTGGGATGGTTTATATGGG
          1 GGGAATGCGATGCTATTGATTATTATTAAGATTTCTCACTGGGATGGTTTATATGGG

                                                                     
        711 GGGAATGCGATGCTATTGATTATTATTAAGATTTCTCACTGGGATGGTTTATATGGG
          1 GGGAATGCGATGCTATTGATTATTATTAAGATTTCTCACTGGGATGGTTTATATGGG

        768 TTGTTCTTTA


Statistics
Matches: 57,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  57   57  1.00

ACGTcount: A:0.25, C:0.09, G:0.28, T:0.39


Consensus pattern (57 bp):   
GGGAATGCGATGCTATTGATTATTATTAAGATTTCTCACTGGGATGGTTTATATGGG

Found at i:1919 original size:2 final size:2

Alignment explanation


    Indices: 1912--1958  Score: 76
    Period size: 2  Copynumber: 23.5  Consensus size: 2

       1902 CCTCCCTTTG

                        *           *                                     
       1912 CT CT CT CT TT CT CT CT TT CT CT CT CT CT CT CT CT CT CT CT CT
          1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT

                   
       1954 CT CT C
          1 CT CT C

       1959 CCCATGTATA


Statistics
Matches: 41,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
   2   41  1.00

ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53


Consensus pattern (2 bp):   
CT

Found at i:1996 original size:4 final size:4

Alignment explanation


    Indices: 1981--2010  Score: 51
    Period size: 4  Copynumber: 7.5  Consensus size: 4

       1971 TTTCTTTGTG

                  *                              
       1981 TGTA TATA TGTA TGTA TGTA TGTA TGTA TG
          1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG

       2011 CATATATATA


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
   4   24  1.00

ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50


Consensus pattern (4 bp):   
TGTA

Found at i:3472 original size:2 final size:2

Alignment explanation


    Indices: 3465--3498  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       3455 ACAGGATTTG

                                                              
       3465 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
          1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT

       3499 TATATATATA


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50


Consensus pattern (2 bp):   
CT

Done.