Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018512.1 Corchorus olitorius cultivar O-4 contig18545, 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: 1960
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32


Found at i:1818 original size:2 final size:2

Alignment explanation


    Indices: 1811--1844  Score: 61
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       1801 ATATAAAGCT

                                                                
       1811 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       1845 TTAAAAGTTA


Statistics
Matches: 31,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   30  0.97

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:1913 original size:6 final size:5

Alignment explanation


    Indices: 1890--1943  Score: 51
    Period size: 5  Copynumber: 10.6  Consensus size: 5

       1880 ATACGAGTAC

                                                                     
       1890 ATAAT ATAAT ATATAT ATAGAT AT-A- ATAAT ATTAAT A-ATAT ATAAT
          1 ATAAT ATAAT ATA-AT ATA-AT ATAAT ATAAT A-TAAT ATA-AT ATAAT

                     
       1936 ATAAT ATA
          1 ATAAT ATA

       1944 CCAAATTAAT


Statistics
Matches: 42,  Mismatches: 1, Indels: 12
        0.76            0.02        0.22

Matches are distributed among these distances:
   3    2  0.05
   4    3  0.07
   5   22  0.52
   6   15  0.36

ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41


Consensus pattern (5 bp):   
ATAAT

Found at i:1943 original size:12 final size:12

Alignment explanation


    Indices: 1893--1943  Score: 61
    Period size: 12  Copynumber: 4.2  Consensus size: 12

       1883 CGAGTACATA

                        
       1893 ATATAATAT-AT
          1 ATATAATATAAT

                         
       1904 ATATAGATATAAT
          1 ATATA-ATATAAT

                 *       
       1917 A-ATATTAATAAT
          1 ATATAAT-ATAAT

                        
       1929 ATATAATATAAT
          1 ATATAATATAAT

               
       1941 ATA
          1 ATA

       1944 CCAAATTAAT


Statistics
Matches: 34,  Mismatches: 2, Indels: 7
        0.79            0.05        0.16

Matches are distributed among these distances:
  11    6  0.18
  12   21  0.62
  13    7  0.21

ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41


Consensus pattern (12 bp):   
ATATAATATAAT
Done.