Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015085.1 Corchorus olitorius cultivar O-4 contig15118, 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: 5337
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34


Found at i:188 original size:25 final size:25

Alignment explanation


    Indices: 142--196  Score: 69
    Period size: 25  Copynumber: 2.2  Consensus size: 25

        132 CTAGAGAAGG

                                     
        142 CTTTTCAAAACAATTTTTTTTTAAA
          1 CTTTTCAAAACAATTTTTTTTTAAA

            *                          
        167 TTTTTC-AAA-AATTTTTGATTTTAAA
          1 CTTTTCAAAACAATTTTT--TTTTAAA

                 
        192 CTTTT
          1 CTTTT

        197 GCTTCTCTAG


Statistics
Matches: 26,  Mismatches: 2, Indels: 4
        0.81            0.06        0.12

Matches are distributed among these distances:
  23    7  0.27
  24    3  0.12
  25   16  0.62

ACGTcount: A:0.33, C:0.09, G:0.02, T:0.56


Consensus pattern (25 bp):   
CTTTTCAAAACAATTTTTTTTTAAA

Found at i:4319 original size:15 final size:15

Alignment explanation


    Indices: 4272--4313  Score: 75
    Period size: 15  Copynumber: 2.8  Consensus size: 15

       4262 GTTTGTTAAA

                           
       4272 TTAAGTACTGAAAAT
          1 TTAAGTACTGAAAAT

                           
       4287 TTAAGTACTGAAAAT
          1 TTAAGTACTGAAAAT

                 *      
       4302 TTAAGCACTGAA
          1 TTAAGTACTGAA

       4314 TCTTTATGGC


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  15   26  1.00

ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31


Consensus pattern (15 bp):   
TTAAGTACTGAAAAT

Found at i:4676 original size:18 final size:18

Alignment explanation


    Indices: 4653--4692  Score: 71
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       4643 GAAATTTTTC

                              
       4653 ATTTTCAATGGTTTGAAA
          1 ATTTTCAATGGTTTGAAA

                             *
       4671 ATTTTCAATGGTTTGAAT
          1 ATTTTCAATGGTTTGAAA

                
       4689 ATTT
          1 ATTT

       4693 AGTTAAAAGA


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  18   21  1.00

ACGTcount: A:0.30, C:0.05, G:0.15, T:0.50


Consensus pattern (18 bp):   
ATTTTCAATGGTTTGAAA
Done.