Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021379.1 Corchorus olitorius cultivar O-4 contig21412, 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: 16202
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:5438 original size:29 final size:30

Alignment explanation


    Indices: 5374--5440  Score: 91
    Period size: 30  Copynumber: 2.3  Consensus size: 30

       5364 GGCTTCGTCT

                     *  *              *  
       5374 TGGACATTGGCACATGAACGAAGAACGTCC
          1 TGGACATTGCCAAATGAACGAAGAACGCCC

                                 *        
       5404 TGGACATTGCCAAATGAAC-ACGAACGCCC
          1 TGGACATTGCCAAATGAACGAAGAACGCCC

                    
       5433 TGGACATT
          1 TGGACATT

       5441 ACCATCGGAA


Statistics
Matches: 33,  Mismatches: 4, Indels: 1
        0.87            0.11        0.03

Matches are distributed among these distances:
  29   16  0.48
  30   17  0.52

ACGTcount: A:0.33, C:0.25, G:0.24, T:0.18


Consensus pattern (30 bp):   
TGGACATTGCCAAATGAACGAAGAACGCCC

Found at i:5451 original size:29 final size:28

Alignment explanation


    Indices: 5396--5489  Score: 80
    Period size: 29  Copynumber: 3.2  Consensus size: 28

       5386 CATGAACGAA

                 *               **      
       5396 GAACGTCCTGGACATTGCCAAATGAACAC
          1 GAACGCCCTGGACATTGCC-ACGGAACAC

                            *            
       5425 GAACGCCCTGGACATTACCATCGGAACAC
          1 GAACGCCCTGGACATTGCCA-CGGAACAC

             **  *       *                
       5454 GTTCGTCCTGGACTTTGCCACAGGAACGAC
          1 GAACGCCCTGGACATTGCCAC-GGAAC-AC

                  
       5484 GAACGC
          1 GAACGC

       5490 TAGGATCTTC


Statistics
Matches: 50,  Mismatches: 12, Indels: 5
        0.75            0.18        0.07

Matches are distributed among these distances:
  28    2  0.04
  29   43  0.86
  30    5  0.10

ACGTcount: A:0.29, C:0.31, G:0.23, T:0.17


Consensus pattern (28 bp):   
GAACGCCCTGGACATTGCCACGGAACAC

Found at i:10089 original size:3 final size:3

Alignment explanation


    Indices: 10081--10109  Score: 58
    Period size: 3  Copynumber: 9.7  Consensus size: 3

      10071 ACCCCTCTCT

                                                  
      10081 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
          1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT

      10110 TGCTTTCCAT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   26  1.00

ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69


Consensus pattern (3 bp):   
TTC

Done.