Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001140.1 Corchorus capsularis cultivar CVL-1 contig01140, 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: 3229
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34


Found at i:1598 original size:20 final size:20

Alignment explanation


    Indices: 1555--1598  Score: 52
    Period size: 20  Copynumber: 2.2  Consensus size: 20

       1545 TAATTTGATT

                          **   *
       1555 TTTTTTTTGCCTTTTTTTTT
          1 TTTTTTTTGCCTTTCATTTG

                      *         
       1575 TTTTTTTTGCGTTTCATTTG
          1 TTTTTTTTGCCTTTCATTTG

                
       1595 TTTT
          1 TTTT

       1599 CAATTTAATC


Statistics
Matches: 20,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.02, C:0.09, G:0.09, T:0.80


Consensus pattern (20 bp):   
TTTTTTTTGCCTTTCATTTG

Found at i:2389 original size:73 final size:73

Alignment explanation


    Indices: 2298--2434  Score: 222
    Period size: 73  Copynumber: 1.9  Consensus size: 73

       2288 CCTCATTAAA

                  *                                                          
       2298 TTAAAATTATTCTCTTAATTAATTAATCTAAATTAAATAAAAATA-TATAGCTCATTAAAATTCT
          1 TTAAAAGTATTCTCTTAATTAATTAATCTAAATTAAATAAAAATACT-TAGCTCATTAAAATTCT

                     
       2362 ATAAGCTGG
         65 ATAAGCTGG

                         *       *     *                                    
       2371 TTAAAAGTATTCTGTTAATTAGTTAATTTAAATTAAATAAAAATACTTAGCTCATTAAAATTCT
          1 TTAAAAGTATTCTCTTAATTAATTAATCTAAATTAAATAAAAATACTTAGCTCATTAAAATTCT

       2435 TCTCTTAATT


Statistics
Matches: 59,  Mismatches: 4, Indels: 2
        0.91            0.06        0.03

Matches are distributed among these distances:
  73   58  0.98
  74    1  0.02

ACGTcount: A:0.45, C:0.09, G:0.06, T:0.41


Consensus pattern (73 bp):   
TTAAAAGTATTCTCTTAATTAATTAATCTAAATTAAATAAAAATACTTAGCTCATTAAAATTCTA
TAAGCTGG
Done.