Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009191.1 Corchorus olitorius cultivar O-4 contig09219, 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, 665

Length: 1109
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.31


Found at i:36 original size:21 final size:21

Alignment explanation


    Indices: 10--123  Score: 158
    Period size: 21  Copynumber: 5.4  Consensus size: 21

          1 GCTAGAAGT

                                 
         10 TCATTGGAGCAAGTTCCAAGC
          1 TCATTGGAGCAAGTTCCAAGC

                                 
         31 TCATTGGAGCAAGTTCCAAGC
          1 TCATTGGAGCAAGTTCCAAGC

                       *        *
         52 TCATTGGAGCAGGTTCCAAGT
          1 TCATTGGAGCAAGTTCCAAGC

                     *           *
         73 TCATTGGAGTAAGGTTCCAAGT
          1 TCATTGGAGCAA-GTTCCAAGC

                            *     
         95 TCATTGGAG-AAGGTTTCAAGC
          1 TCATTGGAGCAA-GTTCCAAGC

                    
        116 TCATTGGA
          1 TCATTGGA

        124 ATTGCCTAAG


Statistics
Matches: 86,  Mismatches: 6, Indels: 2
        0.91            0.06        0.02

Matches are distributed among these distances:
  21   68  0.79
  22   18  0.21

ACGTcount: A:0.27, C:0.18, G:0.26, T:0.28


Consensus pattern (21 bp):   
TCATTGGAGCAAGTTCCAAGC

Found at i:109 original size:43 final size:42

Alignment explanation


    Indices: 6--123  Score: 166
    Period size: 43  Copynumber: 2.8  Consensus size: 42

          1 GCTAG

                                                       
          6 AAGTTCATTGGAGCAA-GTTCCAAGCTCATTGGAGCAAGTTCC
          1 AAGTTCATTGGAG-AAGGTTCCAAGCTCATTGGAGCAAGTTCC

               *         *          *         *        
         48 AAGCTCATTGGAGCAGGTTCCAAGTTCATTGGAGTAAGGTTCC
          1 AAGTTCATTGGAGAAGGTTCCAAGCTCATTGGAGCAA-GTTCC

                               *             
         91 AAGTTCATTGGAGAAGGTTTCAAGCTCATTGGA
          1 AAGTTCATTGGAGAAGGTTCCAAGCTCATTGGA

        124 ATTGCCTAAG


Statistics
Matches: 66,  Mismatches: 8, Indels: 3
        0.86            0.10        0.04

Matches are distributed among these distances:
  41    1  0.02
  42   31  0.47
  43   34  0.52

ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28


Consensus pattern (42 bp):   
AAGTTCATTGGAGAAGGTTCCAAGCTCATTGGAGCAAGTTCC

Found at i:641 original size:19 final size:19

Alignment explanation


    Indices: 617--658  Score: 84
    Period size: 19  Copynumber: 2.2  Consensus size: 19

        607 TTGATTAATA

                               
        617 AAATTGAGGTTTTTTACCC
          1 AAATTGAGGTTTTTTACCC

                               
        636 AAATTGAGGTTTTTTACCC
          1 AAATTGAGGTTTTTTACCC

                
        655 AAAT
          1 AAAT

        659 CAGAGCATAG


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

Matches are distributed among these distances:
  19   23  1.00

ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40


Consensus pattern (19 bp):   
AAATTGAGGTTTTTTACCC

Found at i:853 original size:12 final size:12

Alignment explanation


    Indices: 836--860  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

        826 GGTGGGGGGT

                        
        836 GTGCTTGAAGAG
          1 GTGCTTGAAGAG

                        
        848 GTGCTTGAAGAG
          1 GTGCTTGAAGAG

             
        860 G
          1 G

        861 AGGTGTCATG


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

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.24, C:0.08, G:0.44, T:0.24


Consensus pattern (12 bp):   
GTGCTTGAAGAG
Done.