Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009258.1 Corchorus capsularis cultivar CVL-1 contig09279, 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: 3835
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.30


Found at i:160 original size:12 final size:12

Alignment explanation


    Indices: 143--212  Score: 64
    Period size: 12  Copynumber: 6.3  Consensus size: 12

        133 ACGCGTGGGA

                        
        143 CATCGCACGGGC
          1 CATCGCACGGGC

                   *    
        155 CATCGCATGGGC
          1 CATCGCACGGGC

                        
        167 CAT--C-C-GGC
          1 CATCGCACGGGC

                         
        175 CA-C-CATC-GGC
          1 CATCGCA-CGGGC

                       *
        185 CATCGCACGGGT
          1 CATCGCACGGGC

                        
        197 CATCGCACGGGC
          1 CATCGCACGGGC

                
        209 CATC
          1 CATC

        213 CGGCCACAAC


Statistics
Matches: 48,  Mismatches: 4, Indels: 12
        0.75            0.06        0.19

Matches are distributed among these distances:
   8    6  0.12
  10    7  0.15
  11    2  0.04
  12   33  0.69

ACGTcount: A:0.17, C:0.41, G:0.29, T:0.13


Consensus pattern (12 bp):   
CATCGCACGGGC

Found at i:185 original size:54 final size:55

Alignment explanation


    Indices: 99--212  Score: 140
    Period size: 54  Copynumber: 2.1  Consensus size: 55

         89 GGACCGGCCA

                                    **            **               
         99 CCATCGCATGGAGCAACCCGGCCATGACCGGCCAACGCGTGGGACATCGCACGGG
          1 CCATCGCATGGAGCAACCCGGCCACCACCGGCCAACGCACGGGACATCGCACGGG

                          * *          *      *        *           
        154 CCATCGCATGG-GCCATCCGGCCACCATCGGCCATCGCACGGGTCATCGCACGGG
          1 CCATCGCATGGAGCAACCCGGCCACCACCGGCCAACGCACGGGACATCGCACGGG

                 
        208 CCATC
          1 CCATC

        213 CGGCCACAAC


Statistics
Matches: 50,  Mismatches: 9, Indels: 1
        0.83            0.15        0.02

Matches are distributed among these distances:
  54   39  0.78
  55   11  0.22

ACGTcount: A:0.19, C:0.39, G:0.30, T:0.11


Consensus pattern (55 bp):   
CCATCGCATGGAGCAACCCGGCCACCACCGGCCAACGCACGGGACATCGCACGGG

Found at i:191 original size:42 final size:42

Alignment explanation


    Indices: 143--228  Score: 136
    Period size: 42  Copynumber: 2.0  Consensus size: 42

        133 ACGCGTGGGA

                               *               * *    
        143 CATCGCACGGGCCATCGCATGGGCCATCCGGCCACCATCGGC
          1 CATCGCACGGGCCATCGCACGGGCCATCCGGCCACAACCGGC

                       *                              
        185 CATCGCACGGGTCATCGCACGGGCCATCCGGCCACAACCGGC
          1 CATCGCACGGGCCATCGCACGGGCCATCCGGCCACAACCGGC

              
        227 CA
          1 CA

        229 CTTGACCCTT


Statistics
Matches: 40,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  42   40  1.00

ACGTcount: A:0.19, C:0.43, G:0.28, T:0.10


Consensus pattern (42 bp):   
CATCGCACGGGCCATCGCACGGGCCATCCGGCCACAACCGGC
Done.