Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020205.1 Corchorus olitorius cultivar O-4 contig20238, 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: 14847
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35

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


Found at i:8187 original size:37 final size:37

Alignment explanation


    Indices: 8137--8211  Score: 141
    Period size: 37  Copynumber: 2.0  Consensus size: 37

       8127 TTCAATAGAA

                            *                    
       8137 GTAATTTTTAAACAATCTAAATTTCTTAACGTTCGAC
          1 GTAATTTTTAAACAATATAAATTTCTTAACGTTCGAC

                                                 
       8174 GTAATTTTTAAACAATATAAATTTCTTAACGTTCGAC
          1 GTAATTTTTAAACAATATAAATTTCTTAACGTTCGAC

             
       8211 G
          1 G

       8212 CGTCAGCGCG


Statistics
Matches: 37,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  37   37  1.00

ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40


Consensus pattern (37 bp):   
GTAATTTTTAAACAATATAAATTTCTTAACGTTCGAC

Found at i:10237 original size:21 final size:21

Alignment explanation


    Indices: 10212--10294  Score: 64
    Period size: 22  Copynumber: 3.8  Consensus size: 21

      10202 TATCTTAGAT

                                  
      10212 ATAAT-ATATATTATTAAATAA
          1 ATAATAATATATT-TTAAATAA

                                  
      10233 ATAATAAATATATTTTAAAT-A
          1 ATAAT-AATATATTTTAAATAA

                        *  **      
      10254 ATAAATAATGA-GTTCAAAATAA
          1 AT-AATAAT-ATATTTTAAATAA

                               
      10276 ATTAATAATATATATTTAA
          1 A-TAATAATATAT-TTTAA

      10295 TTACTAAACG


Statistics
Matches: 48,  Mismatches: 6, Indels: 14
        0.71            0.09        0.21

Matches are distributed among these distances:
  21   18  0.38
  22   19  0.40
  23   11  0.23

ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40


Consensus pattern (21 bp):   
ATAATAATATATTTTAAATAA

Found at i:10245 original size:25 final size:25

Alignment explanation


    Indices: 10214--10262  Score: 64
    Period size: 25  Copynumber: 2.0  Consensus size: 25

      10204 TCTTAGATAT

                        *             
      10214 AATATATATT-ATTAAATAAATAATA
          1 AATATATATTAAAT-AATAAATAATA

                   *                
      10239 AATATATTTTAAATAATAAATAAT
          1 AATATATATTAAATAATAAATAAT

      10263 GAGTTCAAAA


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

Matches are distributed among these distances:
  25   19  0.90
  26    2  0.10

ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41


Consensus pattern (25 bp):   
AATATATATTAAATAATAAATAATA

Found at i:11000 original size:2 final size:2

Alignment explanation


    Indices: 10993--11022  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

      10983 TTGGGTAAAG

                                                        
      10993 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      11023 GAATTCTCTG


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:12797 original size:2 final size:2

Alignment explanation


    Indices: 12760--12785  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

      12750 TAACCATTGA

                                                  
      12760 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

      12786 GATTCATATA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

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


Consensus pattern (2 bp):   
AT
Done.