Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023767.1 Corchorus olitorius cultivar O-4 contig23800, 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: 11477
ACGTcount: A:0.32, C:0.24, G:0.23, T:0.21


Found at i:1951 original size:30 final size:30

Alignment explanation


    Indices: 1915--1972  Score: 98
    Period size: 30  Copynumber: 1.9  Consensus size: 30

       1905 AAAGCAGTAG

                          *     *         
       1915 CTGGGCATCCCCCAGAGACTGAACGACTCC
          1 CTGGGCATCCCCCAAAGACTAAACGACTCC

                                        
       1945 CTGGGCATCCCCCAAAGACTAAACGACT
          1 CTGGGCATCCCCCAAAGACTAAACGACT

       1973 TCCTCTCAAA


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  30   26  1.00

ACGTcount: A:0.28, C:0.38, G:0.21, T:0.14


Consensus pattern (30 bp):   
CTGGGCATCCCCCAAAGACTAAACGACTCC

Found at i:5954 original size:27 final size:27

Alignment explanation


    Indices: 5900--5955  Score: 76
    Period size: 27  Copynumber: 2.1  Consensus size: 27

       5890 TAGACTAGGG

                          *  *  *      
       5900 GCGACCCCCCCAGGGGTGCTGCTAGTC
          1 GCGACCCCCCCAGGAGTACTACTAGTC

                                   *   
       5927 GCGACCCCCCCAGGAGTACTACTGGTC
          1 GCGACCCCCCCAGGAGTACTACTAGTC

              
       5954 GC
          1 GC

       5956 CCCCGTTTTT


Statistics
Matches: 25,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  27   25  1.00

ACGTcount: A:0.14, C:0.41, G:0.30, T:0.14


Consensus pattern (27 bp):   
GCGACCCCCCCAGGAGTACTACTAGTC

Found at i:8665 original size:22 final size:22

Alignment explanation


    Indices: 8640--8688  Score: 89
    Period size: 22  Copynumber: 2.2  Consensus size: 22

       8630 GGAAACTACA

                                  
       8640 CTTCGAATTTCGAGGCACGTCG
          1 CTTCGAATTTCGAGGCACGTCG

                  *               
       8662 CTTCGAGTTTCGAGGCACGTCG
          1 CTTCGAATTTCGAGGCACGTCG

                 
       8684 CTTCG
          1 CTTCG

       8689 GGTTCTGGAA


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  22   26  1.00

ACGTcount: A:0.14, C:0.29, G:0.29, T:0.29


Consensus pattern (22 bp):   
CTTCGAATTTCGAGGCACGTCG
Done.