Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016363.1 Corchorus capsularis cultivar CVL-1 contig16384, 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: 11012
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29


Found at i:10167 original size:179 final size:176

Alignment explanation


    Indices: 9846--10343  Score: 515
    Period size: 177  Copynumber: 2.8  Consensus size: 176

       9836 CCATCAATTG

                    *                     *   **                 *           
       9846 AAAA-AACTAATTTTTC-AGAAGCATTTTTTATATATAAAA-ATCAAATTTAGATTTTGACTCCT
          1 AAAACAACAAATTTTTCGA-AAGCATTTTTAATACCTAAAACATCAAATTTA-TTTTTGACT-CT

                      *        * *     **                *                *  
       9908 TCAT-AAAGTCGTAGATCATGCAAGAAAGTTTTAATAGAAACTTTAAAT-ACCTCAATCGGAAAT
         63 TCATGAAAGTTGTAGATCAAGTAAGAACCTTTTAATAGAAAC-TTGAATCACCTCAATCGGACAT

                  *                         **                 
       9971 CTAGAGAAAAAATTATGTTAAATGAAGTTGACTGCCCATTC-CTGCTAACT
        127 CTAGAGCAAAAATTATGTTAAATGAAGTTGACCACCCATTCTC-GCTAACT

                                                                             
      10021 AAAACAACAAATTTTTTCGAAAGCATTTTTAATACCTAAAACATCAAATTTATCTTTTGACTCAT
          1 AAAACAACAAA-TTTTTCGAAAGCATTTTTAATACCTAAAACATCAAATTTAT-TTTTGACTC-T

                       *        *                  *          *     *        
      10086 TCATGAAAGTTATAGATCAAATAAGAACCTTTTAATAGACACTTGAATCAGCTCAACCGGACATC
         63 TCATGAAAGTTGTAGATCAAGTAAGAACCTTTTAATAGAAACTTGAATCACCTCAATCGGACATC

             *    *  *         *  *          *               
      10151 TGGAGCCAATATTATGTTATATTAAGTTGACCATCCATTCTCGCTAACT
        128 TAGAGCAAAAATTATGTTAAATGAAGTTGACCACCCATTCTCGCTAACT

            *           * * * *          *                             *     
      10200 TAAACAACAAATCTCTAGGAAGCATTTTTGATACCTAAAACATCAAATTTAATTTTTGAGT-TCT
          1 AAAACAACAAATTTTTCGAAAGCATTTTTAATACCTAAAACATCAAATTT-ATTTTTGACTCT-T

                            *      *   *                     *      *        
      10264 CATGAAAGTTGTAGATTAAGTAACAACTTTTTAATAGAAACTTGAATCATCTCAATTGGACATCT
         64 CATGAAAGTTGTAGATCAAGTAAGAACCTTTTAATAGAAACTTGAATCACCTCAATCGGACATCT

                           
      10329 AGAGCAAAAATTATG
        129 AGAGCAAAAATTATG

      10344 CAATATTAAA


Statistics
Matches: 267,  Mismatches: 45, Indels: 20
        0.80            0.14        0.06

Matches are distributed among these distances:
 175    4  0.01
 176    6  0.02
 177   94  0.35
 178   70  0.26
 179   92  0.34
 180    1  0.00

ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33


Consensus pattern (176 bp):   
AAAACAACAAATTTTTCGAAAGCATTTTTAATACCTAAAACATCAAATTTATTTTTGACTCTTCA
TGAAAGTTGTAGATCAAGTAAGAACCTTTTAATAGAAACTTGAATCACCTCAATCGGACATCTAG
AGCAAAAATTATGTTAAATGAAGTTGACCACCCATTCTCGCTAACT

Done.