Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013753.1 Corchorus capsularis cultivar CVL-1 contig13774, 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: 8541
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36


Found at i:646 original size:29 final size:29

Alignment explanation


    Indices: 604--661  Score: 107
    Period size: 29  Copynumber: 2.0  Consensus size: 29

        594 TGGTTGGTCA

                            *            
        604 TCAACGCCTCTTGCATTTTGTCATGTGCT
          1 TCAACGCCTCTTGCATCTTGTCATGTGCT

                                         
        633 TCAACGCCTCTTGCATCTTGTCATGTGCT
          1 TCAACGCCTCTTGCATCTTGTCATGTGCT

        662 CCAAGCCCTT


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  29   28  1.00

ACGTcount: A:0.14, C:0.29, G:0.17, T:0.40


Consensus pattern (29 bp):   
TCAACGCCTCTTGCATCTTGTCATGTGCT

Found at i:1915 original size:25 final size:25

Alignment explanation


    Indices: 1887--1940  Score: 72
    Period size: 25  Copynumber: 2.2  Consensus size: 25

       1877 TTAGTTAATT

                                     
       1887 AAATTAGATTGGAACTACATGAATG
          1 AAATTAGATTGGAACTACATGAATG

                  *   *  *        *  
       1912 AAATTATATTTGAGCTACATGACTG
          1 AAATTAGATTGGAACTACATGAATG

                
       1937 AAAT
          1 AAAT

       1941 GCAAACTACT


Statistics
Matches: 25,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  25   25  1.00

ACGTcount: A:0.43, C:0.09, G:0.17, T:0.31


Consensus pattern (25 bp):   
AAATTAGATTGGAACTACATGAATG

Found at i:8443 original size:2 final size:2

Alignment explanation


    Indices: 8438--8541  Score: 201
    Period size: 2  Copynumber: 52.5  Consensus size: 2

       8428 AAAAAGAAAA

                                                                          
       8438 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

                                                                          
       8480 AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

                                           
       8521 AG AG AG AG AG AG AG AG AG AG A
          1 AG AG AG AG AG AG AG AG AG AG A


Statistics
Matches: 101,  Mismatches: 0, Indels: 2
        0.98            0.00        0.02

Matches are distributed among these distances:
   1    1  0.01
   2  100  0.99

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


Consensus pattern (2 bp):   
AG

Done.