Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024506.1 Corchorus olitorius cultivar O-4 contig24539, 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: 4497
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34


Found at i:3485 original size:28 final size:29

Alignment explanation


    Indices: 3415--3495  Score: 101
    Period size: 29  Copynumber: 2.8  Consensus size: 29

       3405 AATAAACTTG

                                 * *     
       3415 AAATGACCAAAATGCCCCTGGTCCTGACA
          1 AAATGACCAAAATGCCCCTGGACATGACA

                                         
       3444 AAATGACCAAAATGCCCCTGGACATGA-A
          1 AAATGACCAAAATGCCCCTGGACATGACA

            *     *  *              
       3472 TAATGATCACAATGCCCCCTGGAC
          1 AAATGACCAAAATG-CCCCTGGAC

       3496 CTAGAAGGAT


Statistics
Matches: 46,  Mismatches: 5, Indels: 2
        0.87            0.09        0.04

Matches are distributed among these distances:
  28   12  0.26
  29   34  0.74

ACGTcount: A:0.36, C:0.30, G:0.17, T:0.17


Consensus pattern (29 bp):   
AAATGACCAAAATGCCCCTGGACATGACA

Found at i:3813 original size:50 final size:50

Alignment explanation


    Indices: 3751--3977  Score: 339
    Period size: 50  Copynumber: 4.5  Consensus size: 50

       3741 CGATCAACTT

                   *     *      *       *  *         *        *
       3751 CTTTGAATTGTCTCCCAATTTAA-CATTTAAGGGACCGTCTCCCGCTTATT
          1 CTTTGAACTGTCTACCAATTCAATC-TTAAAAGGACCGTCTTCCGCTTATC

            *                                         *       
       3801 TTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCTGCTTATC
          1 CTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC

                                                     *        
       3851 CTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTTCGCTTATC
          1 CTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC

                                                              
       3901 CTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
          1 CTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC

                              *        
       3951 CTTTGAACTGTCTACCAACTCAATCTT
          1 CTTTGAACTGTCTACCAATTCAATCTT

       3978 GATATCTGGT


Statistics
Matches: 162,  Mismatches: 14, Indels: 2
        0.91            0.08        0.01

Matches are distributed among these distances:
  50  161  0.99
  51    1  0.01

ACGTcount: A:0.25, C:0.26, G:0.12, T:0.37


Consensus pattern (50 bp):   
CTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC

Done.