Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022251.1 Corchorus olitorius cultivar O-4 contig22284, 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: 10511
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.34

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


Found at i:813 original size:11 final size:12

Alignment explanation


    Indices: 771--819  Score: 59
    Period size: 11  Copynumber: 4.2  Consensus size: 12

        761 GGGGAATCGG

                        
        771 GGAGAGGAAGGA
          1 GGAGAGGAAGGA

                         
        783 CGGAGAGGAA-GA
          1 -GGAGAGGAAGGA

                        
        795 GG-GAGGAAGGA
          1 GGAGAGGAAGGA

                     *  
        806 GGAG-GGAAAGA
          1 GGAGAGGAAGGA

               
        817 GGA
          1 GGA

        820 AGAAAGCCCG


Statistics
Matches: 33,  Mismatches: 1, Indels: 6
        0.82            0.03        0.15

Matches are distributed among these distances:
  10    6  0.18
  11   15  0.45
  12    3  0.09
  13    9  0.27

ACGTcount: A:0.41, C:0.02, G:0.57, T:0.00


Consensus pattern (12 bp):   
GGAGAGGAAGGA

Found at i:4488 original size:31 final size:32

Alignment explanation


    Indices: 4453--4516  Score: 112
    Period size: 32  Copynumber: 2.0  Consensus size: 32

       4443 TCTAATATAA

                                            
       4453 TTAAATTGCTGG-AAAAAAACATAATTTCTTT
          1 TTAAATTGCTGGAAAAAAAACATAATTTCTTT

                    *                       
       4484 TTAAATTGTTGGAAAAAAAACATAATTTCTTT
          1 TTAAATTGCTGGAAAAAAAACATAATTTCTTT

             
       4516 T
          1 T

       4517 GAAAGAATAC


Statistics
Matches: 31,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  31   11  0.35
  32   20  0.65

ACGTcount: A:0.42, C:0.08, G:0.09, T:0.41


Consensus pattern (32 bp):   
TTAAATTGCTGGAAAAAAAACATAATTTCTTT

Found at i:10504 original size:69 final size:70

Alignment explanation


    Indices: 10357--10511  Score: 224
    Period size: 69  Copynumber: 2.2  Consensus size: 70

      10347 CAGATCTTGG

                                          *   *         *                    
      10357 CCAAGTCCTGTCCAGGACTTGGGCTGTTGAGGAATGCAAAAATACAGGACAAGACCTGGGCAGGA
          1 CCAAGTCCTGTCCAGGACTTGGGCTGTTGAAGAACGCAAAAATAAAGGACAAGACCTGGGCAGGA

                 
      10422 GTTAC
         66 GTTAC

                         *       *           *       *           *           
      10427 CCAAGTCCTGTCCCGGACTTGTGCTGTTGAAGAGCGC-AAATTAAAGGACAAGNCCTGGGCAGGA
          1 CCAAGTCCTGTCCAGGACTTGGGCTGTTGAAGAACGCAAAAATAAAGGACAAGACCTGGGCAGGA

                 
      10491 GTTAC
         66 GTTAC

                             
      10496 CCAAGTCCTGT-CAGGA
          1 CCAAGTCCTGTCCAGGA


Statistics
Matches: 76,  Mismatches: 9, Indels: 2
        0.87            0.10        0.02

Matches are distributed among these distances:
  68    4  0.05
  69   40  0.53
  70   32  0.42

ACGTcount: A:0.28, C:0.23, G:0.29, T:0.19


Consensus pattern (70 bp):   
CCAAGTCCTGTCCAGGACTTGGGCTGTTGAAGAACGCAAAAATAAAGGACAAGACCTGGGCAGGA
GTTAC
Done.