Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01005963.1 Corchorus olitorius cultivar O-4 contig05988, 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, 655

Length: 1092
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29


Found at i:409 original size:28 final size:28

Alignment explanation


    Indices: 369--437  Score: 86
    Period size: 28  Copynumber: 2.5  Consensus size: 28

        359 GGTGTCCCTG

                    *                    
        369 AAATGACCCAAATGCCCCTAG-CCTAGCA
          1 AAATGACCAAAATGCCCCTAGACCTA-CA

                               *  **    
        397 AAATGACCAAAATGCCCCTGGATGTACA
          1 AAATGACCAAAATGCCCCTAGACCTACA

                         
        425 AAATGACCAAAAT
          1 AAATGACCAAAAT

        438 AAAAGTAAAT


Statistics
Matches: 36,  Mismatches: 4, Indels: 2
        0.86            0.10        0.05

Matches are distributed among these distances:
  28   34  0.94
  29    2  0.06

ACGTcount: A:0.42, C:0.28, G:0.14, T:0.16


Consensus pattern (28 bp):   
AAATGACCAAAATGCCCCTAGACCTACA

Found at i:790 original size:50 final size:50

Alignment explanation


    Indices: 715--1092  Score: 634
    Period size: 50  Copynumber: 7.6  Consensus size: 50

        705 AACTTATCTA

                           *  *               *             * 
        715 AACTGTCTTCCAATTTAACCTTAAAAGGACCGTCCTCCGCTTATCCTTTG
          1 AACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTCG

                          *  *  *                             
        765 AACTGTCTTCCAATCCACTCATAAAAGGACCGTCTTCCGCTTATCCTTCG
          1 AACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTCG

                 *                                            
        815 AACTGCCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTCG
          1 AACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTCG

                             *                                
        865 AACTGTCTTCCAATTCATTCTTAAAAGGACCGTCTTCCGCTTATCCTTCG
          1 AACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTCG

                                                              
        915 AACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTCG
          1 AACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTCG

                 *                                            
        965 AACTGCCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTCG
          1 AACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTCG

                                                              
       1015 AACTGTCTTCCAATTCAATCTTAAAAGG-CC-TCTTCCGCTTATCCTTCG
          1 AACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTCG

                 *                        
       1063 AACTGCCTTCCGAATTCAATCTTAAAAGGA
          1 AACTGTCTTCC-AATTCAATCTTAAAAGGA


Statistics
Matches: 309,  Mismatches: 17, Indels: 4
        0.94            0.05        0.01

Matches are distributed among these distances:
  48   28  0.09
  49   19  0.06
  50  262  0.85

ACGTcount: A:0.25, C:0.31, G:0.12, T:0.33


Consensus pattern (50 bp):   
AACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTCG

Found at i:872 original size:23 final size:23

Alignment explanation


    Indices: 846--925  Score: 70
    Period size: 23  Copynumber: 3.3  Consensus size: 23

        836 TAAAAGGACC

                                   
        846 GTCTTCCGCTTATCCTTCGAACT
          1 GTCTTCCGCTTATCCTTCGAACT

                   **     *      * *  *
        869 GTCTTCCAATTCATTCTTAAAAGGACC
          1 GTCTTCCGCTT-ATCCTT---CGAACT

                                   
        896 GTCTTCCGCTTATCCTTCGAACT
          1 GTCTTCCGCTTATCCTTCGAACT

                   
        919 GTCTTCC
          1 GTCTTCC

        926 AATTCAATCT


Statistics
Matches: 41,  Mismatches: 12, Indels: 8
        0.67            0.20        0.13

Matches are distributed among these distances:
  23   19  0.46
  24    5  0.12
  26    5  0.12
  27   12  0.29

ACGTcount: A:0.17, C:0.33, G:0.12, T:0.38


Consensus pattern (23 bp):   
GTCTTCCGCTTATCCTTCGAACT

Done.