Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008152.1 Corchorus capsularis cultivar CVL-1 contig08173, 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: 9447
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29


Found at i:967 original size:15 final size:16

Alignment explanation


    Indices: 947--986  Score: 59
    Period size: 14  Copynumber: 2.7  Consensus size: 16

        937 CTGAAAGAAA

                            
        947 CAAATGATTAAA-ACC
          1 CAAATGATTAAACACC

                            
        962 CAAATGA--AAACACC
          1 CAAATGATTAAACACC

                       
        976 CAAATGATTAA
          1 CAAATGATTAA

        987 TCATTTGACG


Statistics
Matches: 22,  Mismatches: 0, Indels: 5
        0.81            0.00        0.19

Matches are distributed among these distances:
  13    3  0.14
  14   10  0.45
  15    7  0.32
  16    2  0.09

ACGTcount: A:0.55, C:0.20, G:0.07, T:0.17


Consensus pattern (16 bp):   
CAAATGATTAAACACC

Found at i:3487 original size:31 final size:31

Alignment explanation


    Indices: 3447--3586  Score: 172
    Period size: 31  Copynumber: 4.5  Consensus size: 31

       3437 ACGGTGTCAG

                                           
       3447 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
          1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC

             *            *                
       3478 ATGTGGCACGCCACATGTACCAAAAAGTGAC
          1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC

              *  *                         
       3509 ACATGTCACGCCACGTGTACCAAAAAGTGAC
          1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC

                    * *   *   **      *  * 
       3540 ACGTGGCATGTCACATGTTTCAAAAAATGGC
          1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC

                    *       
       3571 ACGTGGCATGCCACGT
          1 ACGTGGCACGCCACGT

       3587 TGAACGCCGC


Statistics
Matches: 92,  Mismatches: 17, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  31   92  1.00

ACGTcount: A:0.32, C:0.26, G:0.24, T:0.18


Consensus pattern (31 bp):   
ACGTGGCACGCCACGTGTACCAAAAAGTGAC

Found at i:3584 original size:62 final size:62

Alignment explanation


    Indices: 3447--3586  Score: 190
    Period size: 62  Copynumber: 2.3  Consensus size: 62

       3437 ACGGTGTCAG

                                            *                        *    
       3447 ACGTGGCACGCCACGTGTACCAAAAAGTGACATGTGGCACGCCACATGTACCAAAAAGTGAC
          1 ACGTGGCACGCCACGTGTACCAAAAAGTGACACGTGGCACGCCACATGTACCAAAAAATGAC

              *  *                                 * *       **         * 
       3509 ACATGTCACGCCACGTGTACCAAAAAGTGACACGTGGCATGTCACATGTTTCAAAAAATGGC
          1 ACGTGGCACGCCACGTGTACCAAAAAGTGACACGTGGCACGCCACATGTACCAAAAAATGAC

                    *       
       3571 ACGTGGCATGCCACGT
          1 ACGTGGCACGCCACGT

       3587 TGAACGCCGC


Statistics
Matches: 66,  Mismatches: 12, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  62   66  1.00

ACGTcount: A:0.32, C:0.26, G:0.24, T:0.18


Consensus pattern (62 bp):   
ACGTGGCACGCCACGTGTACCAAAAAGTGACACGTGGCACGCCACATGTACCAAAAAATGAC
Done.