Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002478.1 Corchorus olitorius cultivar O-4 contig02478, 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: 1715
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.30


Found at i:94 original size:27 final size:27

Alignment explanation


    Indices: 52--112  Score: 68
    Period size: 27  Copynumber: 2.3  Consensus size: 27

         42 TCCTCATTAT

                       *    *          
         52 AGGGGTAAAATCGTAATTTTATCAATC
          1 AGGGGTAAAATAGTAAATTTATCAATC

                    *           *  *   
         79 AGGGGTAATATAGTAAATTTGTCCATC
          1 AGGGGTAAAATAGTAAATTTATCAATC

             *     
        106 ACGGGTA
          1 AGGGGTA

        113 TTTTGGTGAT


Statistics
Matches: 28,  Mismatches: 6, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  27   28  1.00

ACGTcount: A:0.34, C:0.11, G:0.23, T:0.31


Consensus pattern (27 bp):   
AGGGGTAAAATAGTAAATTTATCAATC

Found at i:1094 original size:375 final size:375

Alignment explanation


    Indices: 474--1220  Score: 1386
    Period size: 375  Copynumber: 2.0  Consensus size: 375

        464 TGCAGTCCCA

                           *   *                                             
        474 AAAATGGCTATTTTTGACTTATTTCCCTTTAGAATTTCAACTTGCTTTCATCTACAAAGTTATAG
          1 AAAATGGCTATTTTTCACTAATTTCCCTTTAGAATTTCAACTTGCTTTCATCTACAAAGTTATAG

                                                              *              
        539 AGGACTCCAAACCCTACAATTTAGACTCAAGAATGACTCAATTTGGATTCTCTAAGACAAAGTTA
         66 AGGACTCCAAACCCTACAATTTAGACTCAAGAATGACTCAATTTGGATTCACTAAGACAAAGTTA

                                                                             
        604 TGCCCCTCGAAAGAAGGCTGCCCGAAATGAATCTACACTCCCCTGTTTTTCATTTCCAGCAAGGC
        131 TGCCCCTCGAAAGAAGGCTGCCCGAAATGAATCTACACTCCCCTGTTTTTCATTTCCAGCAAGGC

                                     *                                       
        669 GACACTTTGGGAAAATAGACATAACTTCCACAATACACATCCAAATCATGTGATTCCAAAACCAT
        196 GACACTTTGGGAAAATAGACATAACGTCCACAATACACATCCAAATCATGTGATTCCAAAACCAT

                                                                             
        734 TAGAAAGCTAACTCATTAGGCTAAAAATGATATTTAGAAAGCCACTTCAAATTCGAGCTAAAACC
        261 TAGAAAGCTAACTCATTAGGCTAAAAATGATATTTAGAAAGCCACTTCAAATTCGAGCTAAAACC

                                                              
        799 ATTTCAAATTCAACCACCAAGTCAGATTTCCAAAGTTGAACCTCAATTCT
        326 ATTTCAAATTCAACCACCAAGTCAGATTTCCAAAGTTGAACCTCAATTCT

                                                                             
        849 AAAATGGCTATTTTTCACTAATTTCCCTTTAGAATTTCAACTTGCTTTCATCTACAAAGTTATAG
          1 AAAATGGCTATTTTTCACTAATTTCCCTTTAGAATTTCAACTTGCTTTCATCTACAAAGTTATAG

                       *            *                                        
        914 AGGACTCCAAATCCTACAATTTAGGCTCAAGAATGACTCAATTTGGATTCACTAAGACAAAGTTA
         66 AGGACTCCAAACCCTACAATTTAGACTCAAGAATGACTCAATTTGGATTCACTAAGACAAAGTTA

                                                      *             *        
        979 TGCCCCTCGAAAGAAGGCTGCCCGAAATGAATCTACACTCCCTTGTTTTTCATTTCTAGCAAGGC
        131 TGCCCCTCGAAAGAAGGCTGCCCGAAATGAATCTACACTCCCCTGTTTTTCATTTCCAGCAAGGC

                              *                                              
       1044 GACACTTTGGGAAAATAGGCATAACGTCCACAATACACATCCAAATCATGTGATTCCAAAACCAT
        196 GACACTTTGGGAAAATAGACATAACGTCCACAATACACATCCAAATCATGTGATTCCAAAACCAT

                                      *                              *       
       1109 TAGAAAGCTAACTCATTAGGCTAAAACTGATATTTAGAAAGCCACTTCAAATTCGAGTTAAAACC
        261 TAGAAAGCTAACTCATTAGGCTAAAAATGATATTTAGAAAGCCACTTCAAATTCGAGCTAAAACC

                                              *            
       1174 ATTTCAAATTCAACCACCAAGTCAGATTTCCAAATTTGAACCTCAAT
        326 ATTTCAAATTCAACCACCAAGTCAGATTTCCAAAGTTGAACCTCAAT

       1221 CCTGCGATAC


Statistics
Matches: 360,  Mismatches: 12, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
 375  360  1.00

ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29


Consensus pattern (375 bp):   
AAAATGGCTATTTTTCACTAATTTCCCTTTAGAATTTCAACTTGCTTTCATCTACAAAGTTATAG
AGGACTCCAAACCCTACAATTTAGACTCAAGAATGACTCAATTTGGATTCACTAAGACAAAGTTA
TGCCCCTCGAAAGAAGGCTGCCCGAAATGAATCTACACTCCCCTGTTTTTCATTTCCAGCAAGGC
GACACTTTGGGAAAATAGACATAACGTCCACAATACACATCCAAATCATGTGATTCCAAAACCAT
TAGAAAGCTAACTCATTAGGCTAAAAATGATATTTAGAAAGCCACTTCAAATTCGAGCTAAAACC
ATTTCAAATTCAACCACCAAGTCAGATTTCCAAAGTTGAACCTCAATTCT
Done.