Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011731.1 Corchorus capsularis cultivar CVL-1 contig11752, 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: 7069
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.28


Found at i:264 original size:30 final size:31

Alignment explanation


    Indices: 229--359  Score: 113
    Period size: 30  Copynumber: 4.3  Consensus size: 31

        219 TGACACGTGG

                       *                ** 
        229 CACGTGGCATGTCACGTGTCAC-TTTTGGCA
          1 CACGTGGCATGACACGTGTCACTTTTTGATA

                    **                 *   
        259 CACGTGGCGGGACACGTGTCA-TTTTTTATA
          1 CACGTGGCATGACACGTGTCACTTTTTGATA

              **  * *     *            *   
        289 CATATGACGTGACATGTGTCACTTTTTAATA
          1 CACGTGGCATGACACGTGTCACTTTTTGATA

                       *   *            *  
        320 CACGTGGCATGTCACATGTCACTTTTTGGTA
          1 CACGTGGCATGACACGTGTCACTTTTTGATA

                     
        351 CACGTGGCA
          1 CACGTGGCA

        360 GGCCATGTCG


Statistics
Matches: 78,  Mismatches: 21, Indels: 3
        0.76            0.21        0.03

Matches are distributed among these distances:
  30   39  0.50
  31   39  0.50

ACGTcount: A:0.21, C:0.22, G:0.24, T:0.33


Consensus pattern (31 bp):   
CACGTGGCATGACACGTGTCACTTTTTGATA

Found at i:2975 original size:2 final size:2

Alignment explanation


    Indices: 2968--3005  Score: 76
    Period size: 2  Copynumber: 19.0  Consensus size: 2

       2958 AGGTGCTGTC

                                                                    
       2968 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       3006 CAATGGATCA


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   36  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.