Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020267.1 Corchorus olitorius cultivar O-4 contig20300, 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: 5624
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33


Found at i:2770 original size:21 final size:22

Alignment explanation


    Indices: 2724--2775  Score: 65
    Period size: 21  Copynumber: 2.5  Consensus size: 22

       2714 TCCTTACGTA

                                  
       2724 CATAATTA-AAATAAAAAGTTT
          1 CATAATTATAAATAAAAAGTTT

                            *      
       2745 CATAATTATAAAT-AATAGTATT
          1 CATAATTATAAATAAAAAGT-TT

                      
       2767 -ATAATTATA
          1 CATAATTATA

       2776 TATATTATAA


Statistics
Matches: 28,  Mismatches: 1, Indels: 4
        0.85            0.03        0.12

Matches are distributed among these distances:
  21   22  0.79
  22    6  0.21

ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38


Consensus pattern (22 bp):   
CATAATTATAAATAAAAAGTTT

Found at i:2786 original size:15 final size:15

Alignment explanation


    Indices: 2749--2786  Score: 51
    Period size: 15  Copynumber: 2.5  Consensus size: 15

       2739 AAGTTTCATA

                   *       
       2749 ATTATAAATAATAGT
          1 ATTATAATTAATAGT

                            
       2764 ATTATAATTATATA-T
          1 ATTATAATTA-ATAGT

                    
       2779 ATTATAAT
          1 ATTATAAT

       2787 CAAAAAAACT


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  15   18  0.86
  16    3  0.14

ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47


Consensus pattern (15 bp):   
ATTATAATTAATAGT

Found at i:2946 original size:22 final size:23

Alignment explanation


    Indices: 2903--2946  Score: 54
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       2893 ATAATTAATG

                    *        *     
       2903 AAAAAGTTGAATCATCTCAAAAA
          1 AAAAAGTTAAATCATCTAAAAAA

                        *         
       2926 AAAAAGTTAAATGA-CTAAAAA
          1 AAAAAGTTAAATCATCTAAAAA

       2947 GAATACTTAT


Statistics
Matches: 18,  Mismatches: 3, Indels: 1
        0.82            0.14        0.05

Matches are distributed among these distances:
  22    6  0.33
  23   12  0.67

ACGTcount: A:0.61, C:0.09, G:0.09, T:0.20


Consensus pattern (23 bp):   
AAAAAGTTAAATCATCTAAAAAA
Done.