Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010029.1 Corchorus olitorius cultivar O-4 contig10061, 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: 3807
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33


Found at i:3678 original size:2 final size:2

Alignment explanation


    Indices: 3667--3794  Score: 56
    Period size: 2  Copynumber: 66.5  Consensus size: 2

       3657 TAGGATTTTA

                               *       *  *                               
       3667 AT AT AT -T AT AT AA AT AT TT TT AT AT AT AT -T AT AT AT -T AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

             *       *                             *      *            *   
       3706 AA AT AT TT AT AT AT AT AT -T AT A- AT TT AT AA AT AT AT CAG A-
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT

             *  *     *        *                                            
       3746 AA AC AT AA AT CAT TT AT AT AT AT AT AT AT AT A- AT ACT AT -T AT
          1 AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT

               *      
       3788 AT TT AT A
          1 AT AT AT A

       3795 ATTACTTTAA


Statistics
Matches: 94,  Mismatches: 21, Indels: 22
        0.69            0.15        0.16

Matches are distributed among these distances:
   1    8  0.09
   2   81  0.86
   3    5  0.05

ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:3702 original size:30 final size:29

Alignment explanation


    Indices: 3667--3739  Score: 114
    Period size: 28  Copynumber: 2.6  Consensus size: 29

       3657 TAGGATTTTA

                               *          
       3667 ATATATTATATAAATATTTTTATATATATT
          1 ATATATT-TATAAATATTTATATATATATT

                                         
       3697 ATATA-TTATAAATATTTATATATATATT
          1 ATATATTTATAAATATTTATATATATATT

                            
       3725 ATA-ATTTATAAATAT
          1 ATATATTTATAAATAT

       3740 ATCAGAAAAC


Statistics
Matches: 41,  Mismatches: 1, Indels: 4
        0.89            0.02        0.09

Matches are distributed among these distances:
  27    1  0.02
  28   34  0.83
  29    1  0.02
  30    5  0.12

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (29 bp):   
ATATATTTATAAATATTTATATATATATT

Done.