Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003727.1 Corchorus capsularis cultivar CVL-1 contig03735, 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, 631

Length: 1052
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28


Found at i:939 original size:29 final size:31

Alignment explanation


    Indices: 897--989  Score: 100
    Period size: 29  Copynumber: 2.9  Consensus size: 31

        887 ATGTTTATTG

                 *                         
        897 ATCCAAGGCGATCTTTCTTGAGTTAATT-A-
          1 ATCCAGGGCGATCTTTCTTGAGTTAATTAAT

                               *              
        926 ATCCAGGGCGATCTTTCTTCAGTTAATTTCAATT
          1 ATCCAGGGCGATCTTTCTTGAGTTAA-TT-AA-T

                         *                
        960 GATCCAGGGCGATATTTCTTGAGTTTAATT
          1 -ATCCAGGGCGATCTTTCTTGAG-TTAATT

        990 CAGTTGACTA


Statistics
Matches: 53,  Mismatches: 4, Indels: 8
        0.82            0.06        0.12

Matches are distributed among these distances:
  29   24  0.45
  30    2  0.04
  32    1  0.02
  35   22  0.42
  36    4  0.08

ACGTcount: A:0.25, C:0.17, G:0.18, T:0.40


Consensus pattern (31 bp):   
ATCCAGGGCGATCTTTCTTGAGTTAATTAAT

Found at i:965 original size:35 final size:35

Alignment explanation


    Indices: 893--1048  Score: 121
    Period size: 35  Copynumber: 4.6  Consensus size: 35

        883 GTTAATGTTT

                     *             *           
        893 ATTGATCCAAGGCGATCTTTCTTGAG-TTAATT--
          1 ATTGATCCAGGGCGATCTTTCTTCAGCTTAATTCA

                                                
        925 A---ATCCAGGGCGATCTTTCTTCAG-TTAATTTCA
          1 ATTGATCCAGGGCGATCTTTCTTCAGCTTAA-TTCA

                            *      *  *        
        957 ATTGATCCAGGGCGATATTTCTTGAGTTTAATTCA
          1 ATTGATCCAGGGCGATCTTTCTTCAGCTTAATTCA

            *      *      *                *    
        992 GTTGA-CTAGGGCGGTCTTTCTTCAGCTTATTTTCA
          1 ATTGATCCAGGGCGATCTTTCTTCAGCTTA-ATTCA

            *    *      * *       
       1027 GTTGACCCAGGGTGGTCTTTCT
          1 ATTGATCCAGGGCGATCTTTCT

       1049 CCAG


Statistics
Matches: 102,  Mismatches: 13, Indels: 14
        0.79            0.10        0.11

Matches are distributed among these distances:
  29   24  0.24
  30    2  0.02
  32    2  0.02
  34   19  0.19
  35   37  0.36
  36   18  0.18

ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40


Consensus pattern (35 bp):   
ATTGATCCAGGGCGATCTTTCTTCAGCTTAATTCA
Done.