Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008090.1 Corchorus olitorius cultivar O-4 contig08117, whole genome shotgun sequence

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: 4237
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:1755 original size:39 final size:39

Alignment explanation


    Indices: 1710--1798  Score: 142
    Period size: 39  Copynumber: 2.3  Consensus size: 39

       1700 CGAATGTTAC

                                          *        
       1710 GAGGATGAAGATTTTTTGAATGATCCTCTTTATGATGAA
          1 GAGGATGAAGATTTTTTGAATGATCCTCTTCATGATGAA

                                       *           
       1749 GAGGATGAAGATTTTTTGAATGATCCTGTTCATGATGAA
          1 GAGGATGAAGATTTTTTGAATGATCCTCTTCATGATGAA

              *  *     
       1788 GAAGAAGAAGA
          1 GAGGATGAAGA

       1799 AGAATTCCTG


Statistics
Matches: 46,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  39   46  1.00

ACGTcount: A:0.35, C:0.07, G:0.26, T:0.33


Consensus pattern (39 bp):   
GAGGATGAAGATTTTTTGAATGATCCTCTTCATGATGAA

Found at i:2986 original size:14 final size:14

Alignment explanation


    Indices: 2967--3003  Score: 74
    Period size: 14  Copynumber: 2.6  Consensus size: 14

       2957 TATTTCCAAA

                          
       2967 AACAGAAAATTGGC
          1 AACAGAAAATTGGC

                          
       2981 AACAGAAAATTGGC
          1 AACAGAAAATTGGC

                     
       2995 AACAGAAAA
          1 AACAGAAAA

       3004 CAGGAAACAG


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   23  1.00

ACGTcount: A:0.57, C:0.14, G:0.19, T:0.11


Consensus pattern (14 bp):   
AACAGAAAATTGGC

Found at i:3012 original size:14 final size:14

Alignment explanation


    Indices: 2966--3016  Score: 66
    Period size: 14  Copynumber: 3.6  Consensus size: 14

       2956 TTATTTCCAA

                          
       2966 AAACAGAAAATTGG
          1 AAACAGAAAATTGG

            *             
       2980 CAACAGAAAATTGG
          1 AAACAGAAAATTGG

            *         **  
       2994 CAACAGAAAACAGG
          1 AAACAGAAAATTGG

                     
       3008 AAACAGAAA
          1 AAACAGAAA

       3017 CGATGCCAAA


Statistics
Matches: 33,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  14   33  1.00

ACGTcount: A:0.59, C:0.14, G:0.20, T:0.08


Consensus pattern (14 bp):   
AAACAGAAAATTGG
Done.