Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020093.1 Corchorus olitorius cultivar O-4 contig20126, 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: 2454
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.29


Found at i:1908 original size:15 final size:15

Alignment explanation


    Indices: 1888--1935  Score: 54
    Period size: 15  Copynumber: 3.6  Consensus size: 15

       1878 GTTGAAGATG

                           
       1888 TTTTGAGCAAAGCAA
          1 TTTTGAGCAAAGCAA

                           
       1903 TTTT--G---AGCAA
          1 TTTTGAGCAAAGCAA

                           
       1913 -TTTGAGCAAAGCAA
          1 TTTTGAGCAAAGCAA

                     
       1927 TTTTGAGCA
          1 TTTTGAGCA

       1936 TAGATTTGGA


Statistics
Matches: 27,  Mismatches: 0, Indels: 12
        0.69            0.00        0.31

Matches are distributed among these distances:
   9    3  0.11
  10    5  0.19
  11    1  0.04
  13    1  0.04
  14    5  0.19
  15   12  0.44

ACGTcount: A:0.35, C:0.12, G:0.21, T:0.31


Consensus pattern (15 bp):   
TTTTGAGCAAAGCAA

Found at i:1916 original size:24 final size:24

Alignment explanation


    Indices: 1889--1935  Score: 94
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       1879 TTGAAGATGT

                                    
       1889 TTTGAGCAAAGCAATTTTGAGCAA
          1 TTTGAGCAAAGCAATTTTGAGCAA

                                   
       1913 TTTGAGCAAAGCAATTTTGAGCA
          1 TTTGAGCAAAGCAATTTTGAGCA

       1936 TAGATTTGGA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   23  1.00

ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30


Consensus pattern (24 bp):   
TTTGAGCAAAGCAATTTTGAGCAA

Found at i:1998 original size:80 final size:80

Alignment explanation


    Indices: 1907--2069  Score: 326
    Period size: 80  Copynumber: 2.0  Consensus size: 80

       1897 AAGCAATTTT

                                                                             
       1907 GAGCAATTTGAGCAAAGCAATTTTGAGCATAGATTTGGAGATTCGAAGTTCGTGTTTGAAGACCA
          1 GAGCAATTTGAGCAAAGCAATTTTGAGCATAGATTTGGAGATTCGAAGTTCGTGTTTGAAGACCA

                           
       1972 TTTGAAGATAAATTG
         66 TTTGAAGATAAATTG

                                                                             
       1987 GAGCAATTTGAGCAAAGCAATTTTGAGCATAGATTTGGAGATTCGAAGTTCGTGTTTGAAGACCA
          1 GAGCAATTTGAGCAAAGCAATTTTGAGCATAGATTTGGAGATTCGAAGTTCGTGTTTGAAGACCA

                           
       2052 TTTGAAGATAAATTG
         66 TTTGAAGATAAATTG

               
       2067 GAG
          1 GAG

       2070 ACTTGAAGAC


Statistics
Matches: 83,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  80   83  1.00

ACGTcount: A:0.34, C:0.10, G:0.26, T:0.31


Consensus pattern (80 bp):   
GAGCAATTTGAGCAAAGCAATTTTGAGCATAGATTTGGAGATTCGAAGTTCGTGTTTGAAGACCA
TTTGAAGATAAATTG
Done.