Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024083.1 Corchorus olitorius cultivar O-4 contig24116, 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, 976

Length: 1628
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.30


Found at i:764 original size:23 final size:23

Alignment explanation


    Indices: 738--839  Score: 80
    Period size: 23  Copynumber: 4.3  Consensus size: 23

        728 AAAAATTTTC

                                *  
        738 TTTTTTTATGACGCAAAAACTCT
          1 TTTTTTTATGACGCAAAAACACT

                   *     **        *   
        761 TTTTTTTTTAGA-AAAACGCAAAAACT
          1 TTTTTTTAT-GACGCAA---AAACACT

                           *     * 
        787 TTTTTTTATGACGCAGAAACAAT
          1 TTTTTTTATGACGCAAAAACACT

                               * * 
        810 TTTTTTTATGACGCAAAAATAAT
          1 TTTTTTTATGACGCAAAAACACT

                   
        833 TTTTTTT
          1 TTTTTTT

        840 TTCGATGCAA


Statistics
Matches: 61,  Mismatches: 13, Indels: 10
        0.73            0.15        0.12

Matches are distributed among these distances:
  23   43  0.70
  24    2  0.03
  25    2  0.03
  26   14  0.23

ACGTcount: A:0.34, C:0.12, G:0.09, T:0.45


Consensus pattern (23 bp):   
TTTTTTTATGACGCAAAAACACT

Found at i:851 original size:24 final size:23

Alignment explanation


    Indices: 786--839  Score: 90
    Period size: 23  Copynumber: 2.3  Consensus size: 23

        776 ACGCAAAAAC

                            *   *  
        786 TTTTTTTTATGACGCAGAAACAA
          1 TTTTTTTTATGACGCAAAAATAA

                                   
        809 TTTTTTTTATGACGCAAAAATAA
          1 TTTTTTTTATGACGCAAAAATAA

                    
        832 TTTTTTTT
          1 TTTTTTTT

        840 TTCGATGCAA


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  23   29  1.00

ACGTcount: A:0.31, C:0.09, G:0.09, T:0.50


Consensus pattern (23 bp):   
TTTTTTTTATGACGCAAAAATAA

Found at i:1309 original size:16 final size:15

Alignment explanation


    Indices: 1271--1312  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       1261 ACAGAGATTG

                   *       
       1271 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
       1286 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       1301 ACTAGAAAACAA
          1 AC-AGAAAACAA

       1313 AGCAAAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA
Done.