Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017608.1 Corchorus olitorius cultivar O-4 contig17641, 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: 6180
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35


Found at i:317 original size:23 final size:22

Alignment explanation


    Indices: 280--335  Score: 67
    Period size: 23  Copynumber: 2.5  Consensus size: 22

        270 AAGGGATTGG

                                    
        280 CGACTTAAAGAGGAAAAAAATAGT
          1 CGACTT-AAGAGGAAAAAAATA-T

                          **  *   
        304 CGACTTAAGAGGAAGCAATTAT
          1 CGACTTAAGAGGAAAAAAATAT

                      
        326 CGACTTAAGA
          1 CGACTTAAGA

        336 AGAAGCAAGT


Statistics
Matches: 29,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
  22   11  0.38
  23   12  0.41
  24    6  0.21

ACGTcount: A:0.46, C:0.12, G:0.21, T:0.20


Consensus pattern (22 bp):   
CGACTTAAGAGGAAAAAAATAT

Found at i:331 original size:22 final size:23

Alignment explanation


    Indices: 280--351  Score: 76
    Period size: 22  Copynumber: 3.2  Consensus size: 23

        270 AAGGGATTGG

                           **       
        280 CGACTTAAAGAGGAAAAAAATAGT
          1 CGACTT-AAGAGGAAGCAAATAGT

                              *    
        304 CGACTTAAGAGGAAGCAATTA-T
          1 CGACTTAAGAGGAAGCAAATAGT

                      *       *    
        326 CGACTTAAGAAGAAGCAAGT-GT
          1 CGACTTAAGAGGAAGCAAATAGT

                
        348 CGAC
          1 CGAC

        352 AAGAAGGCAA


Statistics
Matches: 42,  Mismatches: 5, Indels: 4
        0.82            0.10        0.08

Matches are distributed among these distances:
  22   24  0.57
  23   12  0.29
  24    6  0.14

ACGTcount: A:0.44, C:0.14, G:0.24, T:0.18


Consensus pattern (23 bp):   
CGACTTAAGAGGAAGCAAATAGT

Found at i:2882 original size:10 final size:10

Alignment explanation


    Indices: 2847--2885  Score: 51
    Period size: 11  Copynumber: 3.7  Consensus size: 10

       2837 AAGTTCGTGT

                       
       2847 TTGAAGACTTA
          1 TTGAAGAC-TA

                      
       2858 TTGAAGACTA
          1 TTGAAGACTA

                     * 
       2868 TTTGAAGACCA
          1 -TTGAAGACTA

                   
       2879 TTGAAGA
          1 TTGAAGA

       2886 ATAATTTCAA


Statistics
Matches: 26,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  10    9  0.35
  11   17  0.65

ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31


Consensus pattern (10 bp):   
TTGAAGACTA

Found at i:2892 original size:22 final size:22

Alignment explanation


    Indices: 2846--2897  Score: 61
    Period size: 22  Copynumber: 2.4  Consensus size: 22

       2836 GAAGTTCGTG

                      *        *  
       2846 TTTGAAGACTTATTGAAGACTA
          1 TTTGAAGACTCATTGAAGAATA

                                   
       2868 TTTGAAGAC-CATTGAAGAATAA
          1 TTTGAAGACTCATTGAAGAAT-A

               *    
       2890 TTTCAAGA
          1 TTTGAAGA

       2898 GCAAGAATTG


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  21    9  0.35
  22   17  0.65

ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33


Consensus pattern (22 bp):   
TTTGAAGACTCATTGAAGAATA
Done.