Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001376.1 Corchorus capsularis cultivar CVL-1 contig01376, 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: 8176
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30


Found at i:1646 original size:69 final size:69

Alignment explanation


    Indices: 1563--1868  Score: 326
    Period size: 69  Copynumber: 4.4  Consensus size: 69

       1553 GTCCATTTAC

                                        *       *           ** *           * 
       1563 TTTTGCAGATTCTGTTCCAAGCACCCCTTCCTACACGGATAACATGTTTTATGGGAAGAGCTCGT
          1 TTTTGCAGATTCTGTTCCAAGCACCCCTGCCTACACAGATAACATGTTCAAGGGGAAGAGCTCAT

                
       1628 CTAA
         66 CTAA

                 **           *           *     *      *               * *   
       1632 TTTTGTGGATTCTGTTCCGAGCACCCCTGCTTACACTGATAACCTGTTCAAGGGGAAGAACGCAT
          1 TTTTGCAGATTCTGTTCCAAGCACCCCTGCCTACACAGATAACATGTTCAAGGGGAAGAGCTCAT

               *
       1697 CTAT
         66 CTAA

                                    *     *  **      *             *  * *    
       1701 TTTTGCAGATTCTGTTCCAAGCACTCCTGCTTATTCAGATAGCATGTTCAAGGGGCAGGGTTCAT
          1 TTTTGCAGATTCTGTTCCAAGCACCCCTGCCTACACAGATAACATGTTCAAGGGGAAGAGCTCAT

              * 
       1766 C-CA
         66 CTAA

                                     *        **                      *      
       1769 TATTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAAAGCTCA
          1 T-TTTGCAGATTCTGTTCCAAGCACCCCTGCCTACACAGATAACATGTTCAAGGGGAAGAGCTCA

                *
       1834 TCTAT
         65 TCTAA

                  *                       
       1839 TTTTGCTGATTCTGTTCCAAGCACCCCTGC
          1 TTTTGCAGATTCTGTTCCAAGCACCCCTGC

       1869 ATATAATTAT


Statistics
Matches: 194,  Mismatches: 41, Indels: 4
        0.81            0.17        0.02

Matches are distributed among these distances:
  68    1  0.01
  69  192  0.99
  70    1  0.01

ACGTcount: A:0.24, C:0.25, G:0.20, T:0.32


Consensus pattern (69 bp):   
TTTTGCAGATTCTGTTCCAAGCACCCCTGCCTACACAGATAACATGTTCAAGGGGAAGAGCTCAT
CTAA
Done.