Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006962.1 Corchorus olitorius cultivar O-4 contig06987, 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, 868

Length: 1448
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27


Found at i:196 original size:13 final size:13

Alignment explanation


    Indices: 178--227  Score: 52
    Period size: 13  Copynumber: 4.1  Consensus size: 13

        168 CTTTCAAAGG

                         
        178 AGAAGAAAGGGGA
          1 AGAAGAAAGGGGA

                         
        191 AGAAGAAA--GG-
          1 AGAAGAAAGGGGA

               **        
        201 AGATCAAAGGGGA
          1 AGAAGAAAGGGGA

             *           
        214 AAAAGAAAGGGGA
          1 AGAAGAAAGGGGA

             
        227 A
          1 A

        228 CAAAGGGGAA


Statistics
Matches: 29,  Mismatches: 5, Indels: 6
        0.73            0.12        0.15

Matches are distributed among these distances:
  10    6  0.21
  11    2  0.07
  12    2  0.07
  13   19  0.66

ACGTcount: A:0.56, C:0.02, G:0.40, T:0.02


Consensus pattern (13 bp):   
AGAAGAAAGGGGA

Found at i:200 original size:23 final size:23

Alignment explanation


    Indices: 173--240  Score: 100
    Period size: 23  Copynumber: 3.0  Consensus size: 23

        163 TTATGCTTTC

                     *             
        173 AAAGGAGAAGAAAGGGGAAGAAG
          1 AAAGGAGAACAAAGGGGAAGAAG

                    *          *   
        196 AAAGGAGATCAAAGGGGAAAAAG
          1 AAAGGAGAACAAAGGGGAAGAAG

                 *                
        219 AAAGGGGAACAAAGGGGAAGAA
          1 AAAGGAGAACAAAGGGGAAGAA

        241 TATCTCAAGT


Statistics
Matches: 39,  Mismatches: 6, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  23   39  1.00

ACGTcount: A:0.56, C:0.03, G:0.40, T:0.01


Consensus pattern (23 bp):   
AAAGGAGAACAAAGGGGAAGAAG
Done.