Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018858.1 Corchorus olitorius cultivar O-4 contig18891, 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: 6785
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23


Found at i:5345 original size:43 final size:42

Alignment explanation


    Indices: 5157--5484  Score: 400
    Period size: 41  Copynumber: 7.8  Consensus size: 42

       5147 AATAACCAAA

                                        *             * 
       5157 AAAGTCCCCAAACACATATATAACACAGGGGCAATTCTAT-TCC
          1 AAAGTCCCCAAACACATATATAACACAGAGGC-A-TCTATATAC

                    *                         *        
       5200 AAAAGTCCTCAAACACATATATAACACAGAGGCACCTATAT-C
          1 -AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATAC

            *                           *   **  *      
       5242 CAAGTCCCCAAACAC--ATATAACACAGGGGCGCCTTTATTAC
          1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATA-TAC

                   *                                  
       5283 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATAT-C
          1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATAC

                                        *               
       5324 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTAT-TAC
          1 AAAGTCCCCAAACACATATATAACACAGAGGC-A-TCTATATAC

                   *                          *       
       5367 AAAGTCCTCAAACACATATATAACACAGAGGCATTTATAT-C
          1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATAC

                                        *       *      
       5408 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
          1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATA-TAC

                   *                          
       5451 AAAGTCCTCAAACACATATATAACACAGAGGCAT
          1 AAAGTCCCCAAACACATATATAACACAGAGGCAT

       5485 TTCTCCTTAT


Statistics
Matches: 248,  Mismatches: 25, Indels: 23
        0.84            0.08        0.08

Matches are distributed among these distances:
  39   19  0.08
  40    1  0.00
  41   98  0.40
  42   11  0.04
  43   89  0.36
  44   30  0.12

ACGTcount: A:0.42, C:0.27, G:0.11, T:0.20


Consensus pattern (42 bp):   
AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATAC

Found at i:5371 original size:84 final size:84

Alignment explanation


    Indices: 5157--5484  Score: 552
    Period size: 84  Copynumber: 3.9  Consensus size: 84

       5147 AATAACCAAA

                                              *      *                       
       5157 AAAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTCCAAAAGTCCTCAAACACATATAT
          1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC-AAAGTCCTCAAACACATATAT

                        *       
       5222 AACACAGAGGCACCTATATC
         65 AACACAGAGGCATCTATATC

            *                               **  *                            
       5242 CAAGTCCCCAAACAC--ATATAACACAGGGGCGCCTTTATTACAAAGTCCTCAAACACATATATA
          1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA

                               
       5305 ACACAGAGGCATCTATATC
         66 ACACAGAGGCATCTATATC

                                                                             
       5324 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
          1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA

                        *      
       5389 ACACAGAGGCATTTATATC
         66 ACACAGAGGCATCTATATC

                                             *                               
       5408 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
          1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA

                        
       5473 ACACAGAGGCAT
         66 ACACAGAGGCAT

       5485 TTCTCCTTAT


Statistics
Matches: 228,  Mismatches: 13, Indels: 5
        0.93            0.05        0.02

Matches are distributed among these distances:
  82   54  0.24
  83   21  0.09
  84  139  0.61
  85   14  0.06

ACGTcount: A:0.42, C:0.27, G:0.11, T:0.20


Consensus pattern (84 bp):   
AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATATC

Done.