Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga03g01226.F4

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: 3471
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30


Found at i:2919 original size:3 final size:3

Alignment explanation


    Indices: 2911--2938  Score: 56
    Period size: 3  Copynumber: 9.3  Consensus size: 3

       2901 ACAGATGCCA

                                                 
       2911 CAG CAG CAG CAG CAG CAG CAG CAG CAG C
          1 CAG CAG CAG CAG CAG CAG CAG CAG CAG C

       2939 TCCCACAGCT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   25  1.00

ACGTcount: A:0.32, C:0.36, G:0.32, T:0.00


Consensus pattern (3 bp):   
CAG

Found at i:2977 original size:15 final size:15

Alignment explanation


    Indices: 2959--2987  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

       2949 GCAACAACAG

                           
       2959 CAGCAGCAACAGCCT
          1 CAGCAGCAACAGCCT

                          
       2974 CAGCAGCAACAGCC
          1 CAGCAGCAACAGCC

       2988 GCTCCCACAT


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:0.34, C:0.41, G:0.21, T:0.03


Consensus pattern (15 bp):   
CAGCAGCAACAGCCT

Found at i:3100 original size:24 final size:24

Alignment explanation


    Indices: 3042--3100  Score: 59
    Period size: 24  Copynumber: 2.5  Consensus size: 24

       3032 AGCAGCAGCA

                                    
       3042 GCAGCAGCAGCAACTCTCCCAGAT
          1 GCAGCAGCAGCAACTCTCCCAGAT

               *  *                 * 
       3066 GCAACAACAGCAGA-TGC-CCCAGTT
          1 GCAGCAGCAGCA-ACT-CTCCCAGAT

                       
       3090 GCAGCAGCAGC
          1 GCAGCAGCAGC

       3101 CACAGCTTGC


Statistics
Matches: 28,  Mismatches: 5, Indels: 4
        0.76            0.14        0.11

Matches are distributed among these distances:
  24   26  0.93
  25    2  0.07

ACGTcount: A:0.31, C:0.36, G:0.24, T:0.10


Consensus pattern (24 bp):   
GCAGCAGCAGCAACTCTCCCAGAT
Done.