Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012554.1 Corchorus olitorius cultivar O-4 contig12587, 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: 19219
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32


Found at i:10 original size:2 final size:2

Alignment explanation


    Indices: 4--46  Score: 79
    Period size: 2  Copynumber: 22.0  Consensus size: 2

          1 GAG

                                                                          
          4 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

              
         45 TA
          1 TA

         47 CACATATTAT


Statistics
Matches: 40,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   39  0.98

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:13372 original size:21 final size:22

Alignment explanation


    Indices: 13333--13373  Score: 57
    Period size: 21  Copynumber: 1.9  Consensus size: 22

      13323 TCAATGCTTT

                         **       
      13333 AGGAATGCAAGAGGGATTTCAA
          1 AGGAATGCAAGAGCCATTTCAA

                                
      13355 AGGAA-GCAAGAGCCATTTC
          1 AGGAATGCAAGAGCCATTTC

      13374 CAAGAAGTTA


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  21   12  0.71
  22    5  0.29

ACGTcount: A:0.39, C:0.15, G:0.29, T:0.17


Consensus pattern (22 bp):   
AGGAATGCAAGAGCCATTTCAA

Found at i:15945 original size:15 final size:16

Alignment explanation


    Indices: 15912--15951  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

      15902 TTACTTTGCT

                            
      15912 TTGTTTTCTAGTATAA
          1 TTGTTTTCTAGTATAA

                        *   
      15928 TTGTTTTCT-GTTTAA
          1 TTGTTTTCTAGTATAA

               *     
      15943 TTGCTTTCT
          1 TTGTTTTCT

      15952 TTCAACCTCT


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  15   13  0.59
  16    9  0.41

ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62


Consensus pattern (16 bp):   
TTGTTTTCTAGTATAA
Done.