Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001762.1 Corchorus olitorius cultivar O-4 contig01762, 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: 13381
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31


Found at i:241 original size:2 final size:2

Alignment explanation


    Indices: 234--279  Score: 92
    Period size: 2  Copynumber: 23.0  Consensus size: 2

        224 ATTCCATGGA

                                                                          
        234 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                 
        276 AT AT
          1 AT AT

        280 CACATATGTA


Statistics
Matches: 44,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   44  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:10894 original size:19 final size:18

Alignment explanation


    Indices: 10867--10908  Score: 57
    Period size: 19  Copynumber: 2.3  Consensus size: 18

      10857 GGAATAATTT

                *             
      10867 TTAAGTAAAAATATAATA
          1 TTAAATAAAAATATAATA

                         *     
      10885 TATAAATAAAAATTTAATA
          1 T-TAAATAAAAATATAATA

                 
      10904 TTAAA
          1 TTAAA

      10909 ATAACTAATT


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  18    5  0.24
  19   16  0.76

ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36


Consensus pattern (18 bp):   
TTAAATAAAAATATAATA

Found at i:10912 original size:19 final size:19

Alignment explanation


    Indices: 10872--10908  Score: 58
    Period size: 19  Copynumber: 2.0  Consensus size: 19

      10862 AATTTTTAAG

                               
      10872 TAAAAATATAATATATAAA
          1 TAAAAATATAATATATAAA

                   *           
      10891 TAAAAATTTAATAT-TAAA
          1 TAAAAATATAATATATAAA

      10909 ATAACTAATT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  18    4  0.24
  19   13  0.76

ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35


Consensus pattern (19 bp):   
TAAAAATATAATATATAAA
Done.