Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007084.1 Corchorus capsularis cultivar CVL-1 contig07105, 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: 8280
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.28


Found at i:2466 original size:11 final size:12

Alignment explanation


    Indices: 2450--2478  Score: 51
    Period size: 12  Copynumber: 2.5  Consensus size: 12

       2440 TATGCAAAAC

                        
       2450 GAAAAAG-TAAA
          1 GAAAAAGATAAA

                        
       2461 GAAAAAGATAAA
          1 GAAAAAGATAAA

                  
       2473 GAAAAA
          1 GAAAAA

       2479 CTAACTAACT


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  11    7  0.41
  12   10  0.59

ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07


Consensus pattern (12 bp):   
GAAAAAGATAAA

Found at i:3785 original size:17 final size:17

Alignment explanation


    Indices: 3763--3805  Score: 50
    Period size: 17  Copynumber: 2.5  Consensus size: 17

       3753 TGAGAAAGAC

                       *   * 
       3763 AAAGAAGAATTTGGGGA
          1 AAAGAAGAATTAGGGCA

                  *          
       3780 AAAGAAAAATTAGGGCA
          1 AAAGAAGAATTAGGGCA

               *     
       3797 AAAAAAGAA
          1 AAAGAAGAA

       3806 AAGAGAACGT


Statistics
Matches: 21,  Mismatches: 5, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  17   21  1.00

ACGTcount: A:0.60, C:0.02, G:0.26, T:0.12


Consensus pattern (17 bp):   
AAAGAAGAATTAGGGCA

Found at i:3845 original size:17 final size:17

Alignment explanation


    Indices: 3823--3861  Score: 51
    Period size: 17  Copynumber: 2.3  Consensus size: 17

       3813 CGTAAAAATA

                             
       3823 TTTTTCGTTTTAATTTT
          1 TTTTTCGTTTTAATTTT

                  *    **    
       3840 TTTTTCTTTTTTGTTTT
          1 TTTTTCGTTTTAATTTT

                 
       3857 TTTTT
          1 TTTTT

       3862 GAAATAATAA


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  17   19  1.00

ACGTcount: A:0.05, C:0.05, G:0.05, T:0.85


Consensus pattern (17 bp):   
TTTTTCGTTTTAATTTT

Found at i:3884 original size:5 final size:5

Alignment explanation


    Indices: 3867--3897  Score: 55
    Period size: 5  Copynumber: 6.4  Consensus size: 5

       3857 TTTTTGAAAT

                                                  
       3867 AATAA AA-AA AATAA AATAA AATAA AATAA AA
          1 AATAA AATAA AATAA AATAA AATAA AATAA AA

       3898 GAAATAAAGT


Statistics
Matches: 25,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   4    4  0.16
   5   21  0.84

ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16


Consensus pattern (5 bp):   
AATAA

Done.