Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021718.1 Corchorus olitorius cultivar O-4 contig21751, 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: 8160
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32


Found at i:2590 original size:18 final size:18

Alignment explanation


    Indices: 2559--2593  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       2549 GTCAAAGTTG

                     *        
       2559 AAGAAAAAATGAAAAAAA
          1 AAGAAAAAAGGAAAAAAA

                 *           
       2577 AAGAAGAAAGGAAAAAA
          1 AAGAAAAAAGGAAAAAA

       2594 TGAAAAAATG


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   15  1.00

ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03


Consensus pattern (18 bp):   
AAGAAAAAAGGAAAAAAA

Found at i:2599 original size:7 final size:8

Alignment explanation


    Indices: 2561--2608  Score: 51
    Period size: 8  Copynumber: 5.8  Consensus size: 8

       2551 CAAAGTTGAA

                    
       2561 GAAAAAAT
          1 GAAAAAAT

                     *
       2569 GAAAAAAAAA
          1 G--AAAAAAT

               *   *
       2579 GAAGAAAG
          1 GAAAAAAT

                    
       2587 GAAAAAAT
          1 GAAAAAAT

                    
       2595 GAAAAAAT
          1 GAAAAAAT

                  
       2603 GAAAAA
          1 GAAAAA

       2609 GAATCAATAA


Statistics
Matches: 33,  Mismatches: 5, Indels: 4
        0.79            0.12        0.10

Matches are distributed among these distances:
   8   26  0.79
  10    7  0.21

ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06


Consensus pattern (8 bp):   
GAAAAAAT

Found at i:6988 original size:25 final size:24

Alignment explanation


    Indices: 6956--7012  Score: 80
    Period size: 25  Copynumber: 2.4  Consensus size: 24

       6946 GTGGATTGTA

                        *            
       6956 AAATAAATTGAATAATTAAGACATT
          1 AAATAAATTGAAGAATTAA-ACATT

                     *              
       6981 AAATAAATTTAAGAATTAAACATT
          1 AAATAAATTGAAGAATTAAACATT

                     
       7005 AAA-AAATT
          1 AAATAAATT

       7013 CAAGGCTGAC


Statistics
Matches: 30,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  23    5  0.17
  24    8  0.27
  25   17  0.57

ACGTcount: A:0.60, C:0.04, G:0.05, T:0.32


Consensus pattern (24 bp):   
AAATAAATTGAAGAATTAAACATT
Done.