Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013324.1 Corchorus olitorius cultivar O-4 contig13357, 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: 4490
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:965 original size:27 final size:27

Alignment explanation


    Indices: 890--972  Score: 121
    Period size: 30  Copynumber: 3.0  Consensus size: 27

        880 ATACCACTAA

                         *             
        890 TAATAATTATTATTATAATAATAAGTT
          1 TAATAATTATTATAATAATAATAAGTT

                      *                   
        917 TAATAATTATAATACCACTAATAATAAGTT
          1 TAATAATTATTATA--A-TAATAATAAGTT

                                      
        947 TAATAATTATTATAATAATAATAAGT
          1 TAATAATTATTATAATAATAATAAGT

        973 CTAAATTAAC


Statistics
Matches: 50,  Mismatches: 3, Indels: 6
        0.85            0.05        0.10

Matches are distributed among these distances:
  27   23  0.46
  28    1  0.02
  29    1  0.02
  30   25  0.50

ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42


Consensus pattern (27 bp):   
TAATAATTATTATAATAATAATAAGTT

Found at i:3987 original size:2 final size:2

Alignment explanation


    Indices: 3974--4026  Score: 70
    Period size: 2  Copynumber: 26.0  Consensus size: 2

       3964 TCCATAAATC

                   *                                         *        *   
       3974 TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA TC TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                           
       4016 TA TA CTA TA TA
          1 TA TA -TA TA TA

       4027 AGTCTAAACT


Statistics
Matches: 44,  Mismatches: 6, Indels: 2
        0.85            0.12        0.04

Matches are distributed among these distances:
   2   42  0.95
   3    2  0.05

ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:4389 original size:30 final size:27

Alignment explanation


    Indices: 4304--4386  Score: 121
    Period size: 30  Copynumber: 3.0  Consensus size: 27

       4294 GTTAATTTAG

                                       
       4304 ACTTATTATTATTATAATAATTATTAA
          1 ACTTATTATTATTATAATAATTATTAA

                              *           
       4331 ACTTATTATTAGTGGTATTATAATTATTAA
          1 ACTTATTATTA-T--TATAATAATTATTAA

                        *             
       4361 ACTTATTATTATAATAATAATTATTA
          1 ACTTATTATTATTATAATAATTATTA

       4387 TTAGTGGATG


Statistics
Matches: 50,  Mismatches: 3, Indels: 6
        0.85            0.05        0.10

Matches are distributed among these distances:
  27   23  0.46
  28    1  0.02
  29    1  0.02
  30   25  0.50

ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51


Consensus pattern (27 bp):   
ACTTATTATTATTATAATAATTATTAA
Done.