Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007935.1 Corchorus olitorius cultivar O-4 contig07962, 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, 689

Length: 1149
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23


Found at i:259 original size:43 final size:42

Alignment explanation


    Indices: 16--260  Score: 329
    Period size: 43  Copynumber: 5.8  Consensus size: 42

          6 ATCTATATCC

                                       *     *       * 
         16 AAGTCCCCAAACACATATATAACACAGGGGCAAATCTATTACA
          1 AAGTCCCCAAACACATATATAACACAGAGGC-ATTCTATTATA

                  **                                   
         59 AAGTCCTGAAACACATATATAACACAGAGGCATT-TA-TATCA
          1 AAGTCCCCAAACACATATATAACACAGAGGCATTCTATTAT-A

                                       *               
        100 AAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTATA
          1 AAGTCCCCAAACACATATATAACACAGAGGCAT-TCTATTATA

                  *                                    
        143 AAGTCCTCAAACACATATATAACACAGAGGCATT-TA-TATCA
          1 AAGTCCCCAAACACATATATAACACAGAGGCATTCTATTAT-A

                                                        
        184 AAGTCCCCAAACACATATATAACACATG-GGCATCTCTATTATA
          1 AAGTCCCCAAACACATATATAACACA-GAGGCAT-TCTATTATA

                  *                           
        227 AAGTCCTCAAACACATATATAACACAGAGGCATT
          1 AAGTCCCCAAACACATATATAACACAGAGGCATT

        261 TCTCCTTATG


Statistics
Matches: 180,  Mismatches: 12, Indels: 21
        0.85            0.06        0.10

Matches are distributed among these distances:
  40    5  0.03
  41   66  0.37
  42    8  0.04
  43   95  0.53
  44    6  0.03

ACGTcount: A:0.42, C:0.24, G:0.11, T:0.23


Consensus pattern (42 bp):   
AAGTCCCCAAACACATATATAACACAGAGGCATTCTATTATA

Found at i:288 original size:84 final size:84

Alignment explanation


    Indices: 9--261  Score: 452
    Period size: 84  Copynumber: 3.0  Consensus size: 84

          1 GAGACATC

                  *                                **       *        *       
          9 TATATCCAAGTCCCCAAACACATATATAACACAGGGGCAAATCTATTACAAAGTCCTGAAACACA
          1 TATATCAAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTATAAAGTCCTCAAACACA

                               
         74 TATATAACACAGAGGCATT
         66 TATATAACACAGAGGCATT

                                                                             
         93 TATATCAAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTATAAAGTCCTCAAACACA
          1 TATATCAAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTATAAAGTCCTCAAACACA

                               
        158 TATATAACACAGAGGCATT
         66 TATATAACACAGAGGCATT

                                             *                               
        177 TATATCAAAGTCCCCAAACACATATATAACACATGGGCATCTCTATTATAAAGTCCTCAAACACA
          1 TATATCAAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTATAAAGTCCTCAAACACA

                               
        242 TATATAACACAGAGGCATT
         66 TATATAACACAGAGGCATT

             
        261 T
          1 T

        262 CTCCTTATGG


Statistics
Matches: 163,  Mismatches: 6, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  84  163  1.00

ACGTcount: A:0.42, C:0.24, G:0.11, T:0.24


Consensus pattern (84 bp):   
TATATCAAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTATAAAGTCCTCAAACACA
TATATAACACAGAGGCATT
Done.