Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013278.1 Corchorus capsularis cultivar CVL-1 contig13299, 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: 22847
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28


Found at i:10294 original size:15 final size:15

Alignment explanation


    Indices: 10274--10311  Score: 58
    Period size: 15  Copynumber: 2.5  Consensus size: 15

      10264 TCATACATAC

                  *     *  
      10274 CCAAATGCCAAATAT
          1 CCAAATACCAAACAT

                           
      10289 CCAAATACCAAACAT
          1 CCAAATACCAAACAT

                    
      10304 CCAAATAC
          1 CCAAATAC

      10312 TGAAATATCC


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  15   21  1.00

ACGTcount: A:0.50, C:0.32, G:0.03, T:0.16


Consensus pattern (15 bp):   
CCAAATACCAAACAT

Found at i:15156 original size:26 final size:25

Alignment explanation


    Indices: 15119--15454  Score: 153
    Period size: 26  Copynumber: 11.8  Consensus size: 25

      15109 CCAATAATTA

                           *          
      15119 AAGTCCTCAAACACTTGGGCATTCAT
          1 AAGTCCTCAAACAC-AGGGCATTCAT

                              *            
      15145 AAGTCC-CTAAACACAGATGCATCTTTCTAT
          1 AAGTCCTC-AAACACAG-GGCA---TTC-AT

                              *          
      15175 CAAAAGTCCTCAAACACCTGGGCATTCAT
          1 ---AAGTCCTCAAACA-CAGGGCATTCAT

                                           
      15204 AAGTCC-CTAAACACAGAGGCATCTTTCTAT
          1 AAGTCCTC-AAACACAG-GGCA---TTC-AT

                              *          
      15234 CAAAAGTCCTCAAACACCTGGGCATTCAT
          1 ---AAGTCCTCAAACA-CAGGGCATTCAT

                                         
      15263 AAGTCC-CTAAACACAGAGGCATCTCTAT
          1 AAGTCCTC-AAACACAG-GGCAT-TC-AT

                              *          
      15291 CAAAAGTCCTCAAACACCTGGGCATTCAT
          1 ---AAGTCCTCAAACA-CAGGGCATTCAT

                                         
      15320 AAGTCC-CTAAACACAGAGGCATTTCTAT
          1 AAGTCCTC-AAACACAG-GGCA-TTC-AT

                                          
      15348 AAAAAAGTCCTCAAACACATGGGCATTCAT
          1 ----AAGTCCTCAAACACA-GGGCATTCAT

                                         *
      15378 AAGTCACT-AAACACAGAGGCATCTCTCAA
          1 AAGTC-CTCAAACACAG-GGCA--T-TCAT

                                       
      15407 AAGTCCTCAAACACAAGGGCAATTCAT
          1 AAGTCCTCAAACAC-AGGGC-ATTCAT

                                  
      15434 AAGTCC-CTAAACACAGAGGCA
          1 AAGTCCTC-AAACACAG-GGCA

      15455 ATTTTCTTCT


Statistics
Matches: 248,  Mismatches: 11, Indels: 102
        0.69            0.03        0.28

Matches are distributed among these distances:
  25   12  0.05
  26   81  0.33
  27   25  0.10
  28    8  0.03
  29   29  0.12
  30   17  0.07
  31   19  0.08
  32   20  0.08
  33   31  0.12
  34    6  0.02

ACGTcount: A:0.37, C:0.28, G:0.14, T:0.22


Consensus pattern (25 bp):   
AAGTCCTCAAACACAGGGCATTCAT

Found at i:15190 original size:59 final size:59

Alignment explanation


    Indices: 15118--15454  Score: 537
    Period size: 59  Copynumber: 5.8  Consensus size: 59

      15108 CCCAATAATT

                           *                            *              
      15118 AAAGTCCTCAAACACTTGGGCATTCATAAGTCCCTAAACACAGATGCATCTTTCTATCA
          1 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATCTTTCTATCA

                                                                       
      15177 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATCTTTCTATCA
          1 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATCTTTCTATCA

                                                                       
      15236 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATC--TCTATCA
          1 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATCTTTCTATCA

                                                                      * 
      15293 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCA--TTTCTATAAA
          1 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATCTTTCTAT-CA

                           *                *                          
      15351 AAAGTCCTCAAACACATGGGCATTCATAAGTCACTAAACACAGAGGCATC--TC--TCA
          1 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATCTTTCTATCA

                           **                                
      15406 AAAGTCCTCAAACACAAGGGCAATTCATAAGTCCCTAAACACAGAGGCA
          1 AAAGTCCTCAAACACCTGGGC-ATTCATAAGTCCCTAAACACAGAGGCA

      15455 ATTTTCTTCT


Statistics
Matches: 264,  Mismatches: 8, Indels: 15
        0.92            0.03        0.05

Matches are distributed among these distances:
  55   21  0.08
  56   27  0.10
  57   60  0.23
  58   49  0.19
  59  107  0.41

ACGTcount: A:0.37, C:0.28, G:0.14, T:0.22


Consensus pattern (59 bp):   
AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATCTTTCTATCA

Done.