Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Gorai.001G045000.3-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, 1000

Length: 2924
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25


Found at i:1732 original size:36 final size:36

Alignment explanation


    Indices: 1624--1735  Score: 113
    Period size: 36  Copynumber: 3.2  Consensus size: 36

       1614 ACTTTCAAAA

                    *  * *        *          *  
       1624 AGAAGCACAAGTAAAAGTCCTGCAAGATCTTCTCGG
          1 AGAAGCACTAGCAGAAGTCCTGTAAGATCTTCTAGG

                   *         *  **       *      
       1660 AGAAGCATTAGCAGAAGCCCCATAAG---GTCTAGG
          1 AGAAGCACTAGCAGAAGTCCTGTAAGATCTTCTAGG

                                                
       1693 AGAAGCACTAGCAGAAGTCCTGTAAGATCTTCTAGG
          1 AGAAGCACTAGCAGAAGTCCTGTAAGATCTTCTAGG

                   
       1729 AGAAGCA
          1 AGAAGCA

       1736 TAAGTAGGAG


Statistics
Matches: 58,  Mismatches: 15, Indels: 6
        0.73            0.19        0.08

Matches are distributed among these distances:
  33   27  0.47
  36   31  0.53

ACGTcount: A:0.37, C:0.21, G:0.25, T:0.18


Consensus pattern (36 bp):   
AGAAGCACTAGCAGAAGTCCTGTAAGATCTTCTAGG

Found at i:2204 original size:12 final size:12

Alignment explanation


    Indices: 2187--2213  Score: 54
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       2177 GCTATGGTCA

                        
       2187 TAGCCCAAGTCG
          1 TAGCCCAAGTCG

                        
       2199 TAGCCCAAGTCG
          1 TAGCCCAAGTCG

               
       2211 TAG
          1 TAG

       2214 TCGAACCTCT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   15  1.00

ACGTcount: A:0.26, C:0.30, G:0.26, T:0.19


Consensus pattern (12 bp):   
TAGCCCAAGTCG

Found at i:2244 original size:36 final size:36

Alignment explanation


    Indices: 2197--2273  Score: 136
    Period size: 36  Copynumber: 2.1  Consensus size: 36

       2187 TAGCCCAAGT

                          *         *           
       2197 CGTAGCCCAAGTCGTAGTCGAACCTCTATTCGCAGC
          1 CGTAGCCCAAGTCGAAGTCGAACCCCTATTCGCAGC

                                                
       2233 CGTAGCCCAAGTCGAAGTCGAACCCCTATTCGCAGC
          1 CGTAGCCCAAGTCGAAGTCGAACCCCTATTCGCAGC

                 
       2269 CGTAG
          1 CGTAG

       2274 TCCAGTAGAT


Statistics
Matches: 39,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  36   39  1.00

ACGTcount: A:0.23, C:0.34, G:0.23, T:0.19


Consensus pattern (36 bp):   
CGTAGCCCAAGTCGAAGTCGAACCCCTATTCGCAGC
Done.