Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009298.1 Corchorus capsularis cultivar CVL-1 contig09319, 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: 21130
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:277 original size:2 final size:2

Alignment explanation


    Indices: 265--299  Score: 54
    Period size: 2  Copynumber: 18.0  Consensus size: 2

        255 ATATAGTAGG

                                                          *      
        265 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AC AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

        300 TTGTGAAAAG


Statistics
Matches: 30,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   29  0.97

ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46


Consensus pattern (2 bp):   
AT

Found at i:1413 original size:28 final size:28

Alignment explanation


    Indices: 1381--1437  Score: 105
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       1371 TATGTTTGAG

                                        
       1381 TTTCATTGATACTTACTCCATCCAAAAT
          1 TTTCATTGATACTTACTCCATCCAAAAT

                           *            
       1409 TTTCATTGATACTTATTCCATCCAAAAT
          1 TTTCATTGATACTTACTCCATCCAAAAT

             
       1437 T
          1 T

       1438 ATCAGTCCTT


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

Matches are distributed among these distances:
  28   28  1.00

ACGTcount: A:0.32, C:0.23, G:0.04, T:0.42


Consensus pattern (28 bp):   
TTTCATTGATACTTACTCCATCCAAAAT

Found at i:17514 original size:21 final size:21

Alignment explanation


    Indices: 17490--17538  Score: 62
    Period size: 21  Copynumber: 2.3  Consensus size: 21

      17480 CAGCTGGGGG

                          * *   *
      17490 CCCATGTGGTATGCTTGGCGC
          1 CCCATGTGGTATGCCTCGCGA

                      *          
      17511 CCCATGTGGTTTGCCTCGCGA
          1 CCCATGTGGTATGCCTCGCGA

                   
      17532 CCCATGT
          1 CCCATGT

      17539 CCTCCAGTGC


Statistics
Matches: 24,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   24  1.00

ACGTcount: A:0.10, C:0.33, G:0.29, T:0.29


Consensus pattern (21 bp):   
CCCATGTGGTATGCCTCGCGA

Found at i:20552 original size:13 final size:13

Alignment explanation


    Indices: 20531--20560  Score: 51
    Period size: 13  Copynumber: 2.3  Consensus size: 13

      20521 GGTGCGTACG

                *        
      20531 GCATGGCATGGGT
          1 GCATAGCATGGGT

                         
      20544 GCATAGCATGGGT
          1 GCATAGCATGGGT

                
      20557 GCAT
          1 GCAT

      20561 GTGTGTTGGC


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  13   16  1.00

ACGTcount: A:0.20, C:0.17, G:0.40, T:0.23


Consensus pattern (13 bp):   
GCATAGCATGGGT
Done.