Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021839.1 Corchorus olitorius cultivar O-4 contig21872, 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, 754

Length: 1257
ACGTcount: A:0.30, C:0.28, G:0.11, T:0.31


Found at i:671 original size:21 final size:21

Alignment explanation


    Indices: 645--759  Score: 176
    Period size: 21  Copynumber: 5.5  Consensus size: 21

        635 TTCGTCTACC

                                 
        645 TGAACCCTCTCTTCATCTTCT
          1 TGAACCCTCTCTTCATCTTCT

             *                * *
        666 TCAACCCTCTCTTCATCTACC
          1 TGAACCCTCTCTTCATCTTCT

                                 
        687 TGAACCCTCTCTTCATCTTCT
          1 TGAACCCTCTCTTCATCTTCT

                              * *
        708 TGAACCCTCTCTTCATCTACC
          1 TGAACCCTCTCTTCATCTTCT

                                 
        729 TGAACCCTCTCTTCATCTTCT
          1 TGAACCCTCTCTTCATCTTCT

             *        
        750 TCAACCCTCT
          1 TGAACCCTCT

        760 GTTGCACAAC


Statistics
Matches: 83,  Mismatches: 11, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   83  1.00

ACGTcount: A:0.17, C:0.42, G:0.03, T:0.38


Consensus pattern (21 bp):   
TGAACCCTCTCTTCATCTTCT

Found at i:692 original size:42 final size:42

Alignment explanation


    Indices: 633--759  Score: 236
    Period size: 42  Copynumber: 3.0  Consensus size: 42

        623 CTCAGAATCA

                 *                                    
        633 TCTTCGTCTACCTGAACCCTCTCTTCATCTTCTTCAACCCTC
          1 TCTTCATCTACCTGAACCCTCTCTTCATCTTCTTCAACCCTC

                                              *       
        675 TCTTCATCTACCTGAACCCTCTCTTCATCTTCTTGAACCCTC
          1 TCTTCATCTACCTGAACCCTCTCTTCATCTTCTTCAACCCTC

                                                      
        717 TCTTCATCTACCTGAACCCTCTCTTCATCTTCTTCAACCCTC
          1 TCTTCATCTACCTGAACCCTCTCTTCATCTTCTTCAACCCTC

             
        759 T
          1 T

        760 GTTGCACAAC


Statistics
Matches: 82,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  42   82  1.00

ACGTcount: A:0.16, C:0.42, G:0.04, T:0.39


Consensus pattern (42 bp):   
TCTTCATCTACCTGAACCCTCTCTTCATCTTCTTCAACCCTC
Done.