Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012248.1 Corchorus olitorius cultivar O-4 contig12281, 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: 14590
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:2935 original size:14 final size:16

Alignment explanation


    Indices: 2916--2947  Score: 50
    Period size: 14  Copynumber: 2.1  Consensus size: 16

       2906 ATTTGTATAA

                            
       2916 ATTTTAAA-AAAT-TT
          1 ATTTTAAATAAATATT

                            
       2930 ATTTTAAATAAATATT
          1 ATTTTAAATAAATATT

              
       2946 AT
          1 AT

       2948 ATCATTAAAA


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  14    8  0.50
  15    4  0.25
  16    4  0.25

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


Consensus pattern (16 bp):   
ATTTTAAATAAATATT

Found at i:3846 original size:21 final size:20

Alignment explanation


    Indices: 3743--3847  Score: 57
    Period size: 21  Copynumber: 5.0  Consensus size: 20

       3733 TCTAACAAAC

                   *   *        
       3743 TTATAAAGTTACTAAAAAAT
          1 TTATAAAATTATTAAAAAAT

            *       *             
       3763 CTACTAAACTTATTAAAAAATT
          1 TTA-TAAAATTATTAAAAAA-T

                         *      *  
       3785 TTATAAGATTATTTTTAAAAGAT
          1 TTATAA-A--ATTATTAAAAAAT

             * *     * *       * 
       3808 TAAAAAAAGGTGTTAAAAATT
          1 TTATAAAA-TTATTAAAAAAT

                               
       3829 TTATAAAATTATTAAAAAA
          1 TTATAAAATTATTAAAAAA

       3848 AACTTATAAG


Statistics
Matches: 61,  Mismatches: 18, Indels: 12
        0.67            0.20        0.13

Matches are distributed among these distances:
  20   11  0.18
  21   31  0.51
  22    5  0.08
  23    5  0.08
  24    9  0.15

ACGTcount: A:0.53, C:0.04, G:0.06, T:0.37


Consensus pattern (20 bp):   
TTATAAAATTATTAAAAAAT

Found at i:13451 original size:42 final size:42

Alignment explanation


    Indices: 13391--13473  Score: 139
    Period size: 42  Copynumber: 2.0  Consensus size: 42

      13381 CCTAAGTCTT

                                                      
      13391 GAAAATTCTCTGTAAATTAAAAAATACTCAACTCAAATCATA
          1 GAAAATTCTCTGTAAATTAAAAAATACTCAACTCAAATCATA

                     *   *      *                    
      13433 GAAAATTCTTTGTTAATTAAGAAATACTCAACTCAAATCAT
          1 GAAAATTCTCTGTAAATTAAAAAATACTCAACTCAAATCAT

      13474 GATCCTTAGC


Statistics
Matches: 38,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  42   38  1.00

ACGTcount: A:0.47, C:0.16, G:0.06, T:0.31


Consensus pattern (42 bp):   
GAAAATTCTCTGTAAATTAAAAAATACTCAACTCAAATCATA

Found at i:13607 original size:55 final size:56

Alignment explanation


    Indices: 13537--13648  Score: 217
    Period size: 56  Copynumber: 2.0  Consensus size: 56

      13527 TTTATTTCGT

                                                                    
      13537 AGAATAATTAAGTAGAGATA-GGGGATAGGATTTATTATAACATTTATTGTGTGAA
          1 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA

                                                                    
      13592 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
          1 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA

             
      13648 A
          1 A

      13649 AGGAAACACA


Statistics
Matches: 56,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
  55   20  0.36
  56   36  0.64

ACGTcount: A:0.40, C:0.02, G:0.24, T:0.34


Consensus pattern (56 bp):   
AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA

Done.