Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018139.1 Corchorus olitorius cultivar O-4 contig18172, 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, 675

Length: 1126
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.33


Found at i:870 original size:322 final size:321

Alignment explanation


    Indices: 163--1126  Score: 1490
    Period size: 322  Copynumber: 3.0  Consensus size: 321

        153 TTATTATAAA

                                         *                *         *        
        163 AAAAACAATTAAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCTTCT-TTTTACCCGAATTTAT
          1 AAAAA-AATTAAAGGGTTTTTCACGCTTCAAATATCGTTTTTCCTTATATTTT--CTGAATTTAT

               *                  *   *                 *                    
        227 TTCAAATTAAATCGAAACAAGAATCAGATGCTCGTAAAAACAAACCCTTTAATCCATTGTGGCTG
         63 TTCGAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTTAATCCATTGTGGCTG

                                                                             
        292 AGATTTGGTTAGATGGATATAGATATTTCAAAGAGTCTTTCTGCCAAAAATCATTCAAAACTGAG
        128 AGATTTGGTTAGATGGATATAGATATTTCAAAGAGTCTTTCTGCCAAAAATCATTCAAAACTGAG

                                               *           *                 
        357 TCGAGGCCCCGAAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTATATGATTTCGGCCAAAAA
        193 TCGAGG-CCCGAAACGCGTTTTTAGCCAAAAACT-CGATGGTTAGTACATGATTTCGGCCAAAAA

                                                               *             
        422 CTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATTTATAATTCAACGC
        256 CTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGC

             
        487 C
        321 C

                * *  *                                   *                   
        488 AAAAGAGTTGAAGGGTTTTTCACGCTTCAAATATCGTTTTTCCTTTTATTTTCTGAATTTATTTC
          1 AAAAAAATTAAAGGGTTTTTCACGCTTCAAATATCGTTTTTCCTTATATTTTCTGAATTTATTTC

                                                                             
        553 GAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTTAATCCATTGTGGCTGAGA
         66 GAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTTAATCCATTGTGGCTGAGA

                                                     *                     * 
        618 TTTGGTTAGATGGATATAGATATTTCAAAGAGTC-TTCTGCAAAAAATCATTCAAAACTGAGTGG
        131 TTTGGTTAGATGGATATAGATATTTCAAAGAGTCTTTCTGCCAAAAATCATTCAAAACTGAGTCG

                                                              *              
        682 AGGCCTCGAAACGCGTTTTTAGCCAAAAACTACGATGGTTAGTACATGATATC-GCCTAAAAACT
        196 AGGCC-CGAAACGCGTTTTTAGCCAAAAACT-CGATGGTTAGTACATGATTTCGGCC-AAAAACT

                             *                   *                      *   
        746 GACCCGAAAAGTTTTTCATCAA-TTTTTGCCACAATATTCAGAAAAAATATATAATTCAATGCC
        258 GACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCC

                                                                             
        809 AAAAAAATTAAAGGGTTTTTCACGCTTCAAATATCGTTTTTCCTATATATTTTCTGAATTTATTT
          1 AAAAAAATTAAAGGGTTTTTCACGCTTCAAATATCGTTTTTCCT-TATATTTTCTGAATTTATTT

                                    *                                        
        874 CGAATTAAATCGAAACAAGATTCATATGCTCGTAAAAACAAATCCTTTAATCCATTGTGGCTGAG
         65 CGAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTTAATCCATTGTGGCTGAG

                                            *                     *          
        939 ATTTGGTTAGATGGATATAGATATTTCAAAGAATCTTTCTGCCAAAAATCATTCTAAACTGAGTC
        130 ATTTGGTTAGATGGATATAGATATTTCAAAGAGTCTTTCTGCCAAAAATCATTCAAAACTGAGTC

                       *         *      *                   * *             *
       1004 GAGGCCCGTAATCGCGTTTTTGGCCAAACAC-CGTTATGGTTAGTACACGTTTTCGGCC-AAAAT
        195 GAGGCCCG-AAACGCGTTTTTAGCCAAAAACTCG--ATGGTTAGTACATGATTTCGGCCAAAAAC

               *                                 *                      
       1067 TGATCCGAAAAGTTTTTCCTCAATTTTTTGCGCACAACACTCAGAAAAAATATATAATTC
        257 TGACCCGAAAAGTTTTTCCTCAATTTTTTGC-CACAATACTCAGAAAAAATATATAATTC


Statistics
Matches: 588,  Mismatches: 40, Indels: 23
        0.90            0.06        0.04

Matches are distributed among these distances:
 321   86  0.15
 322  246  0.42
 323  181  0.31
 324   67  0.11
 325    8  0.01

ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33


Consensus pattern (321 bp):   
AAAAAAATTAAAGGGTTTTTCACGCTTCAAATATCGTTTTTCCTTATATTTTCTGAATTTATTTC
GAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTTAATCCATTGTGGCTGAGA
TTTGGTTAGATGGATATAGATATTTCAAAGAGTCTTTCTGCCAAAAATCATTCAAAACTGAGTCG
AGGCCCGAAACGCGTTTTTAGCCAAAAACTCGATGGTTAGTACATGATTTCGGCCAAAAACTGAC
CCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCC
Done.