Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016094.1 Corchorus capsularis cultivar CVL-1 contig16115, 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: 13323
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35


Found at i:4204 original size:15 final size:16

Alignment explanation


    Indices: 4181--4232  Score: 70
    Period size: 15  Copynumber: 3.2  Consensus size: 16

       4171 AATCAAAATC

                            
       4181 TGAGTTTTAAAATGAT
          1 TGAGTTTTAAAATGAT

                          * 
       4197 TG-GTTTTAAAATGGT
          1 TGAGTTTTAAAATGAT

                              
       4212 TGAAAGTTTTAAAATGAT
          1 TG--AGTTTTAAAATGAT

               
       4230 TGA
          1 TGA

       4233 CAAAGGTTAA


Statistics
Matches: 31,  Mismatches: 2, Indels: 6
        0.79            0.05        0.15

Matches are distributed among these distances:
  15   14  0.45
  16    3  0.10
  18   14  0.45

ACGTcount: A:0.37, C:0.00, G:0.21, T:0.42


Consensus pattern (16 bp):   
TGAGTTTTAAAATGAT

Found at i:6367 original size:27 final size:27

Alignment explanation


    Indices: 6337--6418  Score: 73
    Period size: 27  Copynumber: 3.1  Consensus size: 27

       6327 TGAAGGCAAG

                                       
       6337 CAGCTGGAGATAATCCACTTGCATACT
          1 CAGCTGGAGATAATCCACTTGCATACT

                   *  *    **            
       6364 CAGCTGCTAGCT--TAGACTT-CA-ACTT
          1 CAGCTG-GAGATAATCCACTTGCATAC-T

                                        
       6389 GCAGCTGGAGATAATCCACTTGCATACT
          1 -CAGCTGGAGATAATCCACTTGCATACT

              
       6417 CA
          1 CA

       6419 ACTGCTAGCT


Statistics
Matches: 40,  Mismatches: 8, Indels: 14
        0.65            0.13        0.23

Matches are distributed among these distances:
  24    2  0.05
  25    6  0.15
  26   11  0.28
  27   13  0.32
  28    6  0.15
  29    2  0.05

ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27


Consensus pattern (27 bp):   
CAGCTGGAGATAATCCACTTGCATACT

Found at i:6416 original size:53 final size:53

Alignment explanation


    Indices: 6336--6442  Score: 205
    Period size: 53  Copynumber: 2.0  Consensus size: 53

       6326 ATGAAGGCAA

                                          *                      
       6336 GCAGCTGGAGATAATCCACTTGCATACTCAGCTGCTAGCTTAGACTTCAACTT
          1 GCAGCTGGAGATAATCCACTTGCATACTCAACTGCTAGCTTAGACTTCAACTT

                                                                 
       6389 GCAGCTGGAGATAATCCACTTGCATACTCAACTGCTAGCTTAGACTTCAACTT
          1 GCAGCTGGAGATAATCCACTTGCATACTCAACTGCTAGCTTAGACTTCAACTT

             
       6442 G
          1 G

       6443 ATCTTTCACT


Statistics
Matches: 53,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  53   53  1.00

ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28


Consensus pattern (53 bp):   
GCAGCTGGAGATAATCCACTTGCATACTCAACTGCTAGCTTAGACTTCAACTT
Done.