Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001085.1 Corchorus olitorius cultivar O-4 contig01085, 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, 693

Length: 1155
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.30


Found at i:598 original size:169 final size:168

Alignment explanation


    Indices: 271--613  Score: 388
    Period size: 169  Copynumber: 2.0  Consensus size: 168

        261 TCATTTACCT

                    *                     *                       *          
        271 TTACAATTGGTAGAGATCTGAAATCGGATTGGTGAAAACACTAATGATTGAGAGGATAAAAGAAG
          1 TTACAATTAGTAGAGATCTGAAATCGGATTAGTG---A-ACTAATGATTGAGAGAATAAAAGAAG

                    *     *                                       *    *     
        336 GTAAATTAGAAAACGACTGACAATATTTTTCATTTTAAAAAAATCACCTCACCTGTGATGTATGA
         62 GTAAATTAAAAAACAACTGACAATATTTTTCATTTTAAAAAAATCA-CT--CCTATGATATATGA

                                 *           *           
        401 CCAAATTTTTTCAAAATGTCTGAAATATAAAATGCCTCAAAAGCA
        124 CCAAATTTTTTCAAAATGTCTAAAATATAAAATACCTCAAAAGCA

                                       *                              * **   
        446 TTACAATTAGTAGAGATCTGAAATCGGGTTAGTG-ACTAATGATTGAGAAGAATAGAAGGTTGGT
          1 TTACAATTAGTAGAGATCTGAAATCGGATTAGTGAACTAATGATTGAG-AGAATA-AAAGAAGGT

             *                    *                  *                   *   
        510 ATATTAAAAAACAACTGACATTTTATTTTTCATTTTAAAAAGATCA-T-CTATGATATATGTCCA
         64 AAATTAAAAAACAACTGACA--ATATTTTTCATTTTAAAAAAATCACTCCTATGATATATGACCA

                                                 *    
        573 AATTTTTTCAAAATGT-TCAAAATATAAAATACCTCAGAAGC
        127 AATTTTTTCAAAATGTCT-AAAATATAAAATACCTCAAAAGC

        614 CTGTAAAATG


Statistics
Matches: 145,  Mismatches: 18, Indels: 16
        0.81            0.10        0.09

Matches are distributed among these distances:
 168    1  0.01
 169   49  0.34
 170   13  0.09
 171    5  0.03
 172   24  0.17
 174   22  0.15
 175   31  0.21

ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31


Consensus pattern (168 bp):   
TTACAATTAGTAGAGATCTGAAATCGGATTAGTGAACTAATGATTGAGAGAATAAAAGAAGGTAA
ATTAAAAAACAACTGACAATATTTTTCATTTTAAAAAAATCACTCCTATGATATATGACCAAATT
TTTTCAAAATGTCTAAAATATAAAATACCTCAAAAGCA
Done.