Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006605.1 Corchorus olitorius cultivar O-4 contig06630, 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, 672

Length: 1121
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:184 original size:41 final size:41

Alignment explanation


    Indices: 127--217  Score: 173
    Period size: 41  Copynumber: 2.2  Consensus size: 41

        117 AATATATCAA

                                                     
        127 GCAACGACTAACAAAAGTCGTTGCGAAAAGTTTAAGATTTC
          1 GCAACGACTAACAAAAGTCGTTGCGAAAAGTTTAAGATTTC

                                     *               
        168 GCAACGACTAACAAAAGTCGTTGCGGAAAGTTTAAGATTTC
          1 GCAACGACTAACAAAAGTCGTTGCGAAAAGTTTAAGATTTC

                     
        209 GCAACGACT
          1 GCAACGACT

        218 TAATTTGTCG


Statistics
Matches: 49,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  41   49  1.00

ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23


Consensus pattern (41 bp):   
GCAACGACTAACAAAAGTCGTTGCGAAAAGTTTAAGATTTC

Found at i:312 original size:174 final size:172

Alignment explanation


    Indices: 1--364  Score: 494
    Period size: 174  Copynumber: 2.1  Consensus size: 172

                     *                 *           *             *           
          1 GACTAACAATAGTCGTTGCGAAAAGAGNAAGATTTCACAGCGACTTAATTTGTGGCTTCAAAAGT
          1 GACTAACAAAAGTCGTTGCGAAAAGAGTAAGATTTCACAACGACTTAATTTGTCGCTTCAAAAGT

               *                                                         *   
         66 AATTATGTTTTTGTAGCGACTTCCAAGGTCGCTGCGAAAACCAATTTGTAAAATATATCAAGCAA
         66 AATAATGTTTTTGTAGCGACTTCCAAGGTCGCTGCGAAAACCAATTTGTAAAATATATCAAACAA

                                *     **     *        
        131 CGACTAACAAAAGTCGTTGCGAAAAGTTTAAGATTTCGCAAC
        131 CGACTAACAAAAGTCGTTGCAAAAAGACTAAGAATTCGCAAC

                                *    **         *                  *         
        173 GACTAACAAAAGTCGTTGCGGAAAGTTTAAGATTTCGCAACGACTTAATTTGTCGTTTCAAAAGT
          1 GACTAACAAAAGTCGTTGCGAAAAGAGTAAGATTTCACAACGACTTAATTTGTCGCTTCAAAAGT

                    *               *          *      *                 *   *
        238 AATCAAGTTTTTTTGTAGCGACTTTCAAGGTCGCTTCGAAAATCAATTTGTAAAATATATTAAAT
         66 AAT-AA-TGTTTTTGTAGCGACTTCCAAGGTCGCTGCGAAAACCAATTTGTAAAATATATCAAAC

                                            *           
        303 AACGACTAACAAAAGTCGTTGCAAAAAGACTATGAATTCGCAAC
        129 AACGACTAACAAAAGTCGTTGCAAAAAGACTAAGAATTCGCAAC

                  * *         
        347 GACTAATAGAAGTCGTTG
          1 GACTAACAAAAGTCGTTG

        365 TAAAACTGCT


Statistics
Matches: 166,  Mismatches: 24, Indels: 2
        0.86            0.12        0.01

Matches are distributed among these distances:
 172   59  0.36
 173    1  0.01
 174  106  0.64

ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29


Consensus pattern (172 bp):   
GACTAACAAAAGTCGTTGCGAAAAGAGTAAGATTTCACAACGACTTAATTTGTCGCTTCAAAAGT
AATAATGTTTTTGTAGCGACTTCCAAGGTCGCTGCGAAAACCAATTTGTAAAATATATCAAACAA
CGACTAACAAAAGTCGTTGCAAAAAGACTAAGAATTCGCAAC

Done.