Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010701.1 Corchorus olitorius cultivar O-4 contig10733, 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: 27219
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:5665 original size:25 final size:25

Alignment explanation


    Indices: 5631--5701  Score: 142
    Period size: 25  Copynumber: 2.8  Consensus size: 25

       5621 CCCCCTCGAC

                                     
       5631 CTTATTGTTGGGTAAACGATTACCG
          1 CTTATTGTTGGGTAAACGATTACCG

                                     
       5656 CTTATTGTTGGGTAAACGATTACCG
          1 CTTATTGTTGGGTAAACGATTACCG

                                 
       5681 CTTATTGTTGGGTAAACGATT
          1 CTTATTGTTGGGTAAACGATT

       5702 GTCCCCTCTC


Statistics
Matches: 46,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  25   46  1.00

ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38


Consensus pattern (25 bp):   
CTTATTGTTGGGTAAACGATTACCG

Found at i:6147 original size:13 final size:13

Alignment explanation


    Indices: 6129--6154  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       6119 ATTAGTGTCA

                         
       6129 AATGTGTTATAAT
          1 AATGTGTTATAAT

                         
       6142 AATGTGTTATAAT
          1 AATGTGTTATAAT

       6155 TCATTATTAT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46


Consensus pattern (13 bp):   
AATGTGTTATAAT

Found at i:16833 original size:21 final size:22

Alignment explanation


    Indices: 16807--16862  Score: 87
    Period size: 23  Copynumber: 2.5  Consensus size: 22

      16797 AAAGTTTTTC

                    *             
      16807 TCCTTCAAGC-TCTCGACTGTA
          1 TCCTTCAAACTTCTCGACTGTA

                                   
      16828 TCCTTCAAACTTTCTCGACTGTA
          1 TCCTTCAAAC-TTCTCGACTGTA

                        
      16851 TCCTTCAAACTT
          1 TCCTTCAAACTT

      16863 AACTCCAATC


Statistics
Matches: 32,  Mismatches: 1, Indels: 3
        0.89            0.03        0.08

Matches are distributed among these distances:
  21    9  0.28
  22    2  0.06
  23   21  0.66

ACGTcount: A:0.21, C:0.32, G:0.09, T:0.38


Consensus pattern (22 bp):   
TCCTTCAAACTTCTCGACTGTA

Found at i:16847 original size:23 final size:23

Alignment explanation


    Indices: 16817--16862  Score: 92
    Period size: 23  Copynumber: 2.0  Consensus size: 23

      16807 TCCTTCAAGC

                                   
      16817 TCTCGACTGTATCCTTCAAACTT
          1 TCTCGACTGTATCCTTCAAACTT

                                   
      16840 TCTCGACTGTATCCTTCAAACTT
          1 TCTCGACTGTATCCTTCAAACTT

      16863 AACTCCAATC


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

Matches are distributed among these distances:
  23   23  1.00

ACGTcount: A:0.22, C:0.30, G:0.09, T:0.39


Consensus pattern (23 bp):   
TCTCGACTGTATCCTTCAAACTT
Done.