Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011885.1 Corchorus olitorius cultivar O-4 contig11918, 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: 3867
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35


Found at i:1131 original size:45 final size:45

Alignment explanation


    Indices: 1080--1166  Score: 147
    Period size: 45  Copynumber: 1.9  Consensus size: 45

       1070 AGCAACAATT

                                      *                  
       1080 AATATTAGCTTTATTTTGATGAATTATCTAGACATGGAGGAGTAG
          1 AATATTAGCTTTATTTTGATGAATTACCTAGACATGGAGGAGTAG

                                            *    *    
       1125 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGCGGAG
          1 AATATTAGCTTTATTTTGATGAATTACCTAGACATGGAGGAG

       1167 AATTTCAATA


Statistics
Matches: 39,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  45   39  1.00

ACGTcount: A:0.32, C:0.08, G:0.23, T:0.37


Consensus pattern (45 bp):   
AATATTAGCTTTATTTTGATGAATTACCTAGACATGGAGGAGTAG

Found at i:3404 original size:24 final size:25

Alignment explanation


    Indices: 3354--3405  Score: 79
    Period size: 25  Copynumber: 2.1  Consensus size: 25

       3344 GTGGATTGTA

                        *            
       3354 AAATAAATTGAATAATTAAAACATT
          1 AAATAAATTGAAGAATTAAAACATT

                     *               
       3379 AAATAAATTTAAGAATT-AAACATT
          1 AAATAAATTGAAGAATTAAAACATT

               
       3403 AAA
          1 AAA

       3406 AAGTTCAAGG


Statistics
Matches: 25,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  24   10  0.40
  25   15  0.60

ACGTcount: A:0.62, C:0.04, G:0.04, T:0.31


Consensus pattern (25 bp):   
AAATAAATTGAAGAATTAAAACATT
Done.