Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019413.1 Corchorus olitorius cultivar O-4 contig19446, 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: 8863
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31


Found at i:8389 original size:28 final size:28

Alignment explanation


    Indices: 8316--8490  Score: 197
    Period size: 28  Copynumber: 5.8  Consensus size: 28

       8306 CAATCTTGGG

                                            *
       8316 ATGACAACTTCTGGTGTCAATAATTTCCTCAGC
          1 ATGACAACTTCTGGTGTCAATAATTT--T---T

                                        
       8349 ATGACAACTTCTGGTGTCAATAATTTTT
          1 ATGACAACTTCTGGTGTCAATAATTTTT

                                              
       8377 ATGACAACTTCTGGTGTCAAGATAATAATTTGAT
          1 ATGACAACTTCTGGTGTC-A-ATAAT--TTT--T

                                       *
       8411 ATGACAACTTCTGGTGTCAATAATTTTC
          1 ATGACAACTTCTGGTGTCAATAATTTTT

                                         * 
       8439 ATGACAACTTCTGGTGTCAAGATAATTTAAT
          1 ATGACAACTTCTGGTGTC-A-ATAATTT-TT

                                 
       8470 ATGACAACTTCTGGTGTCAAT
          1 ATGACAACTTCTGGTGTCAAT

       8491 TAAATTTAAA


Statistics
Matches: 129,  Mismatches: 4, Indels: 22
        0.83            0.03        0.14

Matches are distributed among these distances:
  28   36  0.28
  29    4  0.03
  30   16  0.12
  31   19  0.15
  32    8  0.06
  33   27  0.21
  34   19  0.15

ACGTcount: A:0.31, C:0.17, G:0.16, T:0.37


Consensus pattern (28 bp):   
ATGACAACTTCTGGTGTCAATAATTTTT

Found at i:8430 original size:62 final size:59

Alignment explanation


    Indices: 8349--8490  Score: 239
    Period size: 62  Copynumber: 2.4  Consensus size: 59

       8339 TTTCCTCAGC

                                       *                               *  
       8349 ATGACAACTTCTGGTGTCAATAATTTTTATGACAACTTCTGGTGTCAAGATAATAATTTGAT
          1 ATGACAACTTCTGGTGTCAATAATTTTCATGACAACTTCTGGTGTCAAG---ATAATTTAAT

                                                                       
       8411 ATGACAACTTCTGGTGTCAATAATTTTCATGACAACTTCTGGTGTCAAGATAATTTAAT
          1 ATGACAACTTCTGGTGTCAATAATTTTCATGACAACTTCTGGTGTCAAGATAATTTAAT

                                 
       8470 ATGACAACTTCTGGTGTCAAT
          1 ATGACAACTTCTGGTGTCAAT

       8491 TAAATTTAAA


Statistics
Matches: 78,  Mismatches: 2, Indels: 3
        0.94            0.02        0.04

Matches are distributed among these distances:
  59   30  0.38
  62   48  0.62

ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37


Consensus pattern (59 bp):   
ATGACAACTTCTGGTGTCAATAATTTTCATGACAACTTCTGGTGTCAAGATAATTTAAT
Done.