Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019643.1 Corchorus olitorius cultivar O-4 contig19676, 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:0.36, C:0.15, G:0.14, T:0.35


Found at i:1817 original size:15 final size:15

Alignment explanation


    Indices: 1797--1842  Score: 76
    Period size: 15  Copynumber: 3.1  Consensus size: 15

       1787 TCATGTGATA

                           
       1797 TATATATTAACATAT
          1 TATATATTAACATAT

                        *  
       1812 TATATATT-ACAAAT
          1 TATATATTAACATAT

                           
       1826 TATATATTAACATAT
          1 TATATATTAACATAT

              
       1841 TA
          1 TA

       1843 CAAATTATAT


Statistics
Matches: 28,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  14   13  0.46
  15   15  0.54

ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46


Consensus pattern (15 bp):   
TATATATTAACATAT

Found at i:1827 original size:14 final size:14

Alignment explanation


    Indices: 1797--1834  Score: 58
    Period size: 14  Copynumber: 2.6  Consensus size: 14

       1787 TCATGTGATA

                        *  
       1797 TATATATTAACATAT
          1 TATATATT-ACAAAT

                          
       1812 TATATATTACAAAT
          1 TATATATTACAAAT

                     
       1826 TATATATTA
          1 TATATATTA

       1835 ACATATTACA


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  14   14  0.64
  15    8  0.36

ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47


Consensus pattern (14 bp):   
TATATATTACAAAT

Found at i:2899 original size:31 final size:31

Alignment explanation


    Indices: 2850--3009  Score: 160
    Period size: 31  Copynumber: 5.2  Consensus size: 31

       2840 ACGGTGTCTG

                    *    *             *   
       2850 ACGTGGCATGCCATGTGTACCAAAAAGCGAC
          1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC

             *                             
       2881 ATGTGGCACGCCACGTGTA-CAAAAAGTGAC
          1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC

             *       *    *              * 
       2911 ATGTGGCACACCACATGTACCAAAAAGTGGC
          1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC

                 * *  *   *    *           
       2942 ACGTGACCCGTCACATGTATCAAAAAGTGAC
          1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC

                **       *    *            
       2973 ACGTATCACGCCATGTGTGCCAAAAAGTGAC
          1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC

                  
       3004 ACGTGG
          1 ACGTGG

       3010 TATGCCTCGT


Statistics
Matches: 104,  Mismatches: 24, Indels: 2
        0.80            0.18        0.02

Matches are distributed among these distances:
  30   27  0.26
  31   77  0.74

ACGTcount: A:0.33, C:0.25, G:0.24, T:0.17


Consensus pattern (31 bp):   
ACGTGGCACGCCACGTGTACCAAAAAGTGAC

Done.