Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019182.1 Corchorus olitorius cultivar O-4 contig19215, 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: 5045
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.37


Found at i:434 original size:30 final size:29

Alignment explanation


    Indices: 391--447  Score: 89
    Period size: 30  Copynumber: 1.9  Consensus size: 29

        381 TTAGGATTAG

                                         
        391 TTATTTATGCTTTAATTTTCAA-TTTCCT
          1 TTATTTATGCTTTAATTTTCAAGTTTCCT

                                         
        419 TTATCTTATGTCTTTAATTTTCAAGTTTC
          1 TTAT-TTATG-CTTTAATTTTCAAGTTTC

        448 ATTAATAAAC


Statistics
Matches: 26,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  28    4  0.15
  29    5  0.19
  30   13  0.50
  31    4  0.15

ACGTcount: A:0.21, C:0.14, G:0.05, T:0.60


Consensus pattern (29 bp):   
TTATTTATGCTTTAATTTTCAAGTTTCCT

Found at i:746 original size:27 final size:27

Alignment explanation


    Indices: 716--771  Score: 112
    Period size: 27  Copynumber: 2.1  Consensus size: 27

        706 GAACCTAGGA

                                       
        716 TAGAATTTGATTGTTTTTGATTGATCT
          1 TAGAATTTGATTGTTTTTGATTGATCT

                                       
        743 TAGAATTTGATTGTTTTTGATTGATCT
          1 TAGAATTTGATTGTTTTTGATTGATCT

              
        770 TA
          1 TA

        772 TTTCCCCAAT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   29  1.00

ACGTcount: A:0.23, C:0.04, G:0.18, T:0.55


Consensus pattern (27 bp):   
TAGAATTTGATTGTTTTTGATTGATCT

Found at i:2017 original size:19 final size:18

Alignment explanation


    Indices: 1993--2028  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       1983 TGAAGACTTA

                               
       1993 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
       2012 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

       2029 ATTATTTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28


Consensus pattern (18 bp):   
TTGAAGACAATTGAAGAT
Done.