Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010542.1 Corchorus olitorius cultivar O-4 contig10574, 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, 905

Length: 1509
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.37


Found at i:122 original size:69 final size:68

Alignment explanation


    Indices: 5--219  Score: 279
    Period size: 69  Copynumber: 3.1  Consensus size: 68

          1 AGAG

                                                      *                      
          5 TTGATCTCGTTTCAAGAAGGTTTTATGATCAGAGTTGATCTCCTTTCAAGTAAGTTTTTGATGAT
          1 TTGATCTCGTTTCAAGAA-GTTTTATGATCAGAGTTGATCTCATTTCAAG-AAGTTTTTGATGAT

                 
         70 CAGAA
         64 CAGAA

                                         *                            *      
         75 TTGAT-TCGTTTCAAGAAGTTTTGATGATTAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATC
          1 TTGATCTCGTTTCAAGAAGTTTT-ATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTGATGATC

               *
        139 AGAG
         65 AGAA

                    *                                      *           **   *
        143 TTGATCTCATTTCAAGAAGTTTTTTTATGATCAGAGTTGATCTCATTCCAAGAAGTTTTCAATGG
          1 TTGATCTCGTTTCAAGAAG---TTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTGATGA

                 *
        208 TCAGAG
         63 TCAGAA

                  
        214 TTGATC
          1 TTGATC

        220 CCCAAAAGAT


Statistics
Matches: 130,  Mismatches: 10, Indels: 9
        0.87            0.07        0.06

Matches are distributed among these distances:
  68   27  0.21
  69   48  0.37
  70    5  0.04
  71   46  0.35
  72    4  0.03

ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41


Consensus pattern (68 bp):   
TTGATCTCGTTTCAAGAAGTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTGATGATCA
GAA

Found at i:144 original size:35 final size:35

Alignment explanation


    Indices: 1--219  Score: 291
    Period size: 35  Copynumber: 6.3  Consensus size: 35

                        *           *          
          1 AGAGTTGATCTCGTTTCAAGAAG-GTTTTATGATC
          1 AGAGTTGATCTCATTTCAAGAAGTTTTTTATGATC

                        *                *      
         35 AGAGTTGATCTCCTTTCAAGTAAGTTTTTGATGATC
          1 AGAGTTGATCTCATTTCAAG-AAGTTTTTTATGATC

               *        *               *     *
         71 AGAATTGAT-TCGTTTCAAGAAG-TTTTGATGATT
          1 AGAGTTGATCTCATTTCAAGAAGTTTTTTATGATC

                                               
        104 AGAGTTGATCTCATTTCAAGAAGTTTTTTATGATC
          1 AGAGTTGATCTCATTTCAAGAAGTTTTTTATGATC

                                                
        139 AGAGTTGATCTCATTTCAAGAAGTTTTTTTATGATC
          1 AGAGTTGATCTCATTTCAAGAAG-TTTTTTATGATC

                           *           **   *  
        175 AGAGTTGATCTCATTCCAAGAAGTTTTCAATGGTC
          1 AGAGTTGATCTCATTTCAAGAAGTTTTTTATGATC

                      
        210 AGAGTTGATC
          1 AGAGTTGATC

        220 CCCAAAAGAT


Statistics
Matches: 166,  Mismatches: 14, Indels: 9
        0.88            0.07        0.05

Matches are distributed among these distances:
  33   18  0.11
  34   34  0.20
  35   63  0.38
  36   51  0.31

ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40


Consensus pattern (35 bp):   
AGAGTTGATCTCATTTCAAGAAGTTTTTTATGATC
Done.