Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021733.1 Corchorus olitorius cultivar O-4 contig21766, 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, 769

Length: 1282
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35


Found at i:697 original size:290 final size:287

Alignment explanation


    Indices: 207--1093  Score: 1555
    Period size: 287  Copynumber: 3.1  Consensus size: 287

        197 TGGGTAAGTT

                *        * *                                                 
        207 ATCGGTTCAAGTACGTATTAAGTCTT-AGAACGTATGGCGTGTATGATCATATGTCGGCAACAAT
          1 ATCGTTTCAAGTAAGCATTAAGTCTTCA-AACGTATGGCGTGTATGATCATATGTCGGCAACAAT

                                                         *          *        
        271 GCACCGGATCCAATGAGATGTGCTTATATATATTTATTATGCGAAGACTGATGGGTTCGATCATA
         65 GCACCGGATCCAATGAGATGTGCTTATATATATTTATTATGCGAATACTGATGGGTGCGATCATA

             *  *                                                            
        336 CCAGTACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTAC
        130 CTAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTAC

                        *                                                    
        401 TAGGATGGGTGATCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTTTTCATTTTTATTTTCTTTTC
        195 TAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCC-TTTTTCA-TTTTATTTTCTTTTC

                                *         
        466 TTCTTCTTTCGAAATTTCTTTTGGTAGACA
        258 TTCTTCTTTCGAAATTTCTTATGGTAGACA

                                                                             
        496 ATCGTTTCAAGTAAGCATTAAGTCTTCAAACGTATGGCGTGTATGATCATATGTCGGGCAACAAT
          1 ATCGTTTCAAGTAAGCATTAAGTCTTCAAACGTATGGCGTGTATGATCATATGTC-GGCAACAAT

                *         *                                                  
        561 GCACTGGATCCAATTAGATGTGCTTATATATATTTATTATGCGAATACTGATGGGTGCGATCATA
         65 GCACCGGATCCAATGAGATGTGCTTATATATATTTATTATGCGAATACTGATGGGTGCGATCATA

                    *                                                        
        626 CTAGCACTTATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTAC
        130 CTAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTAC

                                                                             
        691 TAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTTTCATTTTATTTTCTTTTCTT
        195 TAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTTTCATTTTATTTTCTTTTCTT

                                        
        756 CTTCTTTCGAAATTTCTTATGGTAGACA
        260 CTTCTTTCGAAATTTCTTATGGTAGACA

                                            *       *                        
        784 ATCGTTTCAAGTAAGCATTAAGTCTTCAAACGAATGGCGTTTATGATCATATGTCGGCAACAATG
          1 ATCGTTTCAAGTAAGCATTAAGTCTTCAAACGTATGGCGTGTATGATCATATGTCGGCAACAATG

                                                     *   *                   
        849 CACCGGATCCAATGAGATGTGCTTATATATATTTATTATGCAAATTCTGATGGGTGCGATCATA-
         66 CACCGGATCCAATGAGATGTGCTTATATATATTTATTATGCGAATACTGATGGGTGCGATCATAC

                                     *                                       
        913 TCAGCACTAATGCACCGGATCCCATTAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTAC
        131 T-AGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTAC

                                                                             
        978 TAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTTTCATTTTA-TTTCTTTTCTT
        195 TAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTTTCATTTTATTTTCTTTTCTT

                                        
       1042 CTTCTTTCGAAATTTCTTATGGTAGACA
        260 CTTCTTTCGAAATTTCTTATGGTAGACA

                                    
       1070 ATCGTTTCAAGTAAGCATTAAGTC
          1 ATCGTTTCAAGTAAGCATTAAGTC

       1094 CTAGTATGGC


Statistics
Matches: 575,  Mismatches: 20, Indels: 9
        0.95            0.03        0.01

Matches are distributed among these distances:
 286   64  0.11
 287  184  0.32
 288   97  0.17
 289   57  0.10
 290  173  0.30

ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34


Consensus pattern (287 bp):   
ATCGTTTCAAGTAAGCATTAAGTCTTCAAACGTATGGCGTGTATGATCATATGTCGGCAACAATG
CACCGGATCCAATGAGATGTGCTTATATATATTTATTATGCGAATACTGATGGGTGCGATCATAC
TAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACT
AGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTTTCATTTTATTTTCTTTTCTTC
TTCTTTCGAAATTTCTTATGGTAGACA

Done.