Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011038.1 Corchorus capsularis cultivar CVL-1 contig11059, 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: 5282
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33


Found at i:174 original size:16 final size:17

Alignment explanation


    Indices: 158--208  Score: 50
    Period size: 16  Copynumber: 2.9  Consensus size: 17

        148 AAGAGTGAAA

                              *
        158 ATAATAGATAAATAAAAAG
          1 ATAATAGATAAAT--AAAC

                       *      
        177 ATAAATAGATATATAAAC
          1 AT-AATAGATAAATAAAC

                           
        195 A-AATAGATAAATAA
          1 ATAATAGATAAATAA

        209 GTATGTAAAC


Statistics
Matches: 28,  Mismatches: 3, Indels: 5
        0.78            0.08        0.14

Matches are distributed among these distances:
  16   12  0.43
  18    4  0.14
  19    2  0.07
  20   10  0.36

ACGTcount: A:0.67, C:0.02, G:0.08, T:0.24


Consensus pattern (17 bp):   
ATAATAGATAAATAAAC

Found at i:261 original size:12 final size:12

Alignment explanation


    Indices: 156--260  Score: 68
    Period size: 12  Copynumber: 8.8  Consensus size: 12

        146 AAAAGAGTGA

                     *  
        156 AAAT-AATAGAT
          1 AAATAAATATAT

                   * *  
        167 AAATAAAAAGAT
          1 AAATAAATATAT

                 *      
        179 AAATAGATATAT
          1 AAATAAATATAT

               *     *  
        191 AAACAAATAGAT
          1 AAATAAATATAT

                  *   * 
        203 AAATAAGTATGT
          1 AAATAAATATAT

                *        
        215 AAACAAAATATAT
          1 AAA-TAAATATAT

             *   *     *
        228 ATATATATATAC
          1 AAATAAATATAT

                 *   *  
        240 AAATATATAAAT
          1 AAATAAATATAT

                     
        252 AAATAAATA
          1 AAATAAATA

        261 ATAGCTTAAT


Statistics
Matches: 70,  Mismatches: 22, Indels: 3
        0.74            0.23        0.03

Matches are distributed among these distances:
  11    4  0.06
  12   58  0.83
  13    8  0.11

ACGTcount: A:0.64, C:0.03, G:0.06, T:0.28


Consensus pattern (12 bp):   
AAATAAATATAT
Done.