Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016201.1 Corchorus olitorius cultivar O-4 contig16234, 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: 2065
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.34


Found at i:1186 original size:177 final size:175

Alignment explanation


    Indices: 819--1202  Score: 479
    Period size: 177  Copynumber: 2.2  Consensus size: 175

        809 TTCCACCATA

                        *                                  *    *            
        819 AGCACAAATTATGTAATATTAAGTAGACCGTCTATCCGTTAACCGAATCAACTAATTCTTTGGAA
          1 AGCA-AAATTATATAATATTAAGTAGACCGTCTATCCGTTAACCGAAACAACAAATTCTTTGGAA

                    *                                                        
        884 GCATTTTTTATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGA
         65 GCATTTTTGATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGA

                           *      **    *  *  *      *    
        949 AACAACCTTTCAAGAGACACTTGGATCATCTCAATCAGACATCCGG
        130 AACAACCTTTCAAGAAACACTTAAATCACCTAAAGCAGACAACCGG

                                    *                   *                    
        995 AGCAAAAGTTATATAATATTAAGTGGACCGTCTATTCCCGTTAATCGAAACAACAAATT-TTTCG
          1 AGCAAAA-TTATATAATATTAAGTAGACCGTCTA-T-CCGTTAACCGAAACAACAAATTCTTT-G

                                                                             
       1059 GAAGCATTTTTGATA-CTTGAAACATTAAA-TTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATC
         62 GAAGCATTTTTGATACCTTG-AACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATC

               *     *    *  *                      *  *        
       1122 ATGGAACAATCTTTTAATAAACACTTAAATCACCTAAAGCGGATAACCGAGG
        126 ATGAAACAACCTTTCAAGAAACACTTAAATCACCTAAAGCAGACAACC--GG

                            *    *        
       1174 AG-AAAATTATATAATGTTAAATAGACCGT
          1 AGCAAAATTATATAATATTAAGTAGACCGT

       1203 TTAGCCAAAC


Statistics
Matches: 179,  Mismatches: 22, Indels: 13
        0.84            0.10        0.06

Matches are distributed among these distances:
 175    3  0.02
 176   28  0.16
 177   97  0.54
 178   47  0.26
 179    4  0.02

ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32


Consensus pattern (175 bp):   
AGCAAAATTATATAATATTAAGTAGACCGTCTATCCGTTAACCGAAACAACAAATTCTTTGGAAG
CATTTTTGATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGAA
ACAACCTTTCAAGAAACACTTAAATCACCTAAAGCAGACAACCGG
Done.