Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017646.1 Corchorus olitorius cultivar O-4 contig17679, 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: 3703
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.34


Found at i:684 original size:31 final size:31

Alignment explanation


    Indices: 643--789  Score: 152
    Period size: 31  Copynumber: 4.7  Consensus size: 31

        633 GACGTGGCTT

                 *             *           
        643 GCCACATGTACCAAAAAGCAACATGTAGCAC
          1 GCCACGTGTACCAAAAAGCGACATGTAGCAC

                                 *          
        674 GCCACGTGTACCAAAAAGCGATATG-AGGCAC
          1 GCCACGTGTACCAAAAAGCGACATGTA-GCAC

                              *        *   
        705 GCCACGTGTACCAAAAAGTGACATGTATCAC
          1 GCCACGTGTACCAAAAAGCGACATGTAGCAC

                *       *     *       *   *
        736 GCCATGTGTACCCAAAAGTGACATGTGGCAT
          1 GCCACGTGTACCAAAAAGCGACATGTAGCAC

                *    **       *    
        767 GCCATGTGTTTCAAAAAGTGACA
          1 GCCACGTGTACCAAAAAGCGACA

        790 CATGGCATGC


Statistics
Matches: 100,  Mismatches: 14, Indels: 4
        0.85            0.12        0.03

Matches are distributed among these distances:
  30    1  0.01
  31   98  0.98
  32    1  0.01

ACGTcount: A:0.35, C:0.24, G:0.22, T:0.18


Consensus pattern (31 bp):   
GCCACGTGTACCAAAAAGCGACATGTAGCAC

Found at i:745 original size:62 final size:62

Alignment explanation


    Indices: 643--789  Score: 177
    Period size: 62  Copynumber: 2.4  Consensus size: 62

        633 GACGTGGCTT

                 *            **                                *         
        643 GCCACATGTACCAAAAAGCAACATGTAGCACGCCACGTGTACCAAAAAGCGATATGAGGCAC
          1 GCCACGTGTACCAAAAAGTGACATGTAGCACGCCACGTGTACCAAAAAGCGACATGAGGCAC

                                       *       *       *     *      *    *
        705 GCCACGTGTACCAAAAAGTGACATGTATCACGCCATGTGTACCCAAAAGTGACATGTGGCAT
          1 GCCACGTGTACCAAAAAGTGACATGTAGCACGCCACGTGTACCAAAAAGCGACATGAGGCAC

                *    **            
        767 GCCATGTGTTTCAAAAAGTGACA
          1 GCCACGTGTACCAAAAAGTGACA

        790 CATGGCATGC


Statistics
Matches: 72,  Mismatches: 13, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  62   72  1.00

ACGTcount: A:0.35, C:0.24, G:0.22, T:0.18


Consensus pattern (62 bp):   
GCCACGTGTACCAAAAAGTGACATGTAGCACGCCACGTGTACCAAAAAGCGACATGAGGCAC

Found at i:2754 original size:6 final size:6

Alignment explanation


    Indices: 2740--2780  Score: 64
    Period size: 6  Copynumber: 6.7  Consensus size: 6

       2730 AGATCTTACA

                       *                                   
       2740 ATATCT ATATTT ATATCT ATATCT ATATCT ATATACT ATAT
          1 ATATCT ATATCT ATATCT ATATCT ATATCT ATAT-CT ATAT

       2781 AAGTCTAAAC


Statistics
Matches: 32,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
   6   26  0.81
   7    6  0.19

ACGTcount: A:0.37, C:0.12, G:0.00, T:0.51


Consensus pattern (6 bp):   
ATATCT

Found at i:3138 original size:21 final size:21

Alignment explanation


    Indices: 3097--3140  Score: 54
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       3087 TTATTAGTGG

                     *  *        
       3097 TATTATAATTATTTAACTTAT
          1 TATTATAATAATATAACTTAT

                                  
       3118 TATTATAATAATAATAA-TTAT
          1 TATTATAATAAT-ATAACTTAT

              
       3139 TA
          1 TA

       3141 GTGGTATGTA


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  21   17  0.85
  22    3  0.15

ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52


Consensus pattern (21 bp):   
TATTATAATAATATAACTTAT

Found at i:3139 original size:30 final size:27

Alignment explanation


    Indices: 3049--3132  Score: 105
    Period size: 30  Copynumber: 3.0  Consensus size: 27

       3039 TTTCACGTTA

                                        
       3049 ATTTAGACTTATTATTATTATAATAATT
          1 ATTTA-ACTTATTATTATTATAATAATT

               *                   *      
       3077 ATTAAACTTATTATTAGTGGTATTATAATT
          1 ATTTAACTTATTATTA-T--TATAATAATT

                             *        
       3107 ATTTAACTTATTATTATAATAATAAT
          1 ATTTAACTTATTATTATTATAATAAT

       3133 AATTATTAGT


Statistics
Matches: 48,  Mismatches: 5, Indels: 7
        0.80            0.08        0.12

Matches are distributed among these distances:
  27   18  0.38
  28    5  0.10
  29    1  0.02
  30   24  0.50

ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51


Consensus pattern (27 bp):   
ATTTAACTTATTATTATTATAATAATT
Done.