Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023100.1 Corchorus olitorius cultivar O-4 contig23133, 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: 39331
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35


Found at i:9832 original size:15 final size:15

Alignment explanation


    Indices: 9814--9844  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       9804 ATCTAAGGAT

                           
       9814 TATATATATAATATA
          1 TATATATATAATATA

                      *    
       9829 TATATATATATTATA
          1 TATATATATAATATA

             
       9844 T
          1 T

       9845 TTGAGCCGGT


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (15 bp):   
TATATATATAATATA

Found at i:29535 original size:39 final size:39

Alignment explanation


    Indices: 29492--29566  Score: 150
    Period size: 39  Copynumber: 1.9  Consensus size: 39

      29482 GTTTAGTTTG

                                                   
      29492 CTAATTATAAGTTAATTGGGTTGAATCCATATAAAACAT
          1 CTAATTATAAGTTAATTGGGTTGAATCCATATAAAACAT

                                                
      29531 CTAATTATAAGTTAATTGGGTTGAATCCATATAAAA
          1 CTAATTATAAGTTAATTGGGTTGAATCCATATAAAA

      29567 TATTTTGTTA


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  39   36  1.00

ACGTcount: A:0.41, C:0.09, G:0.13, T:0.36


Consensus pattern (39 bp):   
CTAATTATAAGTTAATTGGGTTGAATCCATATAAAACAT

Found at i:30927 original size:25 final size:25

Alignment explanation


    Indices: 30869--30928  Score: 66
    Period size: 25  Copynumber: 2.4  Consensus size: 25

      30859 AATTTTCCAT

                       *     *     **
      30869 CAAAGAAGAAGGGAGAATAAGAAGG
          1 CAAAGAAGAAGAGAGAAAAAGAACA

            *   *                    
      30894 TAAACAAGAAGAGAGAAAAAGAACA
          1 CAAAGAAGAAGAGAGAAAAAGAACA

                      
      30919 CAAAGAAGAA
          1 CAAAGAAGAA

      30929 AAGAAGAATA


Statistics
Matches: 27,  Mismatches: 8, Indels: 0
        0.77            0.23        0.00

Matches are distributed among these distances:
  25   27  1.00

ACGTcount: A:0.63, C:0.07, G:0.27, T:0.03


Consensus pattern (25 bp):   
CAAAGAAGAAGAGAGAAAAAGAACA

Found at i:32430 original size:42 final size:42

Alignment explanation


    Indices: 32383--32465  Score: 157
    Period size: 42  Copynumber: 2.0  Consensus size: 42

      32373 AGCAACAATT

                                      *               
      32383 AATATTAGCTTTATTTTGATGAATTATCTAGAGATGGAGTAG
          1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAG

                                                     
      32425 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTA
          1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTA

      32466 TTAGAATTAG


Statistics
Matches: 40,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  42   40  1.00

ACGTcount: A:0.34, C:0.06, G:0.20, T:0.40


Consensus pattern (42 bp):   
AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAG
Done.