Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Gorai.010G078900.6-JGI_221_v2.1

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, 921

Length: 1535
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23


Found at i:1186 original size:12 final size:12

Alignment explanation


    Indices: 1125--1177  Score: 67
    Period size: 12  Copynumber: 4.7  Consensus size: 12

       1115 TGATCATCAT

                        
       1125 CAGCAACAGCAG
          1 CAGCAACAGCAG

                 *      
       1137 CAGCACCAGCAG
          1 CAGCAACAGCAG

                        
       1149 CAGCAACA--A-
          1 CAGCAACAGCAG

                       *
       1158 CAGCAACAGCAA
          1 CAGCAACAGCAG

                    
       1170 CAGCAACA
          1 CAGCAACA

       1178 TCATCAGCAT


Statistics
Matches: 36,  Mismatches: 2, Indels: 6
        0.82            0.05        0.14

Matches are distributed among these distances:
   9    8  0.22
  10    1  0.03
  11    1  0.03
  12   26  0.72

ACGTcount: A:0.45, C:0.36, G:0.19, T:0.00


Consensus pattern (12 bp):   
CAGCAACAGCAG

Found at i:1189 original size:6 final size:6

Alignment explanation


    Indices: 1125--1177  Score: 58
    Period size: 6  Copynumber: 9.3  Consensus size: 6

       1115 TGATCATCAT

                        *      *      *                            
       1125 CAGCAA CAGCAG CAGCAC CAGCAG CAGC-A -A-CAA CAGCAA CAGCAA
          1 CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA

                     
       1170 CAGCAA CA
          1 CAGCAA CA

       1178 TCATCAGCAT


Statistics
Matches: 40,  Mismatches: 4, Indels: 6
        0.80            0.08        0.12

Matches are distributed among these distances:
   3    1  0.03
   4    2  0.05
   5    1  0.03
   6   36  0.90

ACGTcount: A:0.45, C:0.36, G:0.19, T:0.00


Consensus pattern (6 bp):   
CAGCAA
Done.