Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017825.1 Corchorus olitorius cultivar O-4 contig17858, 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: 19845
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26


Found at i:518 original size:42 final size:40

Alignment explanation


    Indices: 459--542  Score: 141
    Period size: 42  Copynumber: 2.0  Consensus size: 40

        449 ATACCTAAGA

                                                      
        459 ATTTAATTAATGTAAGTATTTCAGTTATTATAGTATTATTAC
          1 ATTTAATTAATGTAAGTATTTCAGTTATTATA-TA-TATTAC

                                 *                  
        501 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
          1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

              
        541 AT
          1 AT

        543 AGGAATTAAA


Statistics
Matches: 41,  Mismatches: 1, Indels: 2
        0.93            0.02        0.05

Matches are distributed among these distances:
  40    8  0.20
  41    2  0.05
  42   31  0.76

ACGTcount: A:0.37, C:0.04, G:0.08, T:0.51


Consensus pattern (40 bp):   
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

Found at i:5727 original size:40 final size:40

Alignment explanation


    Indices: 5665--5745  Score: 126
    Period size: 40  Copynumber: 2.0  Consensus size: 40

       5655 ACTTGATCCT

                     *       *                      
       5665 CCTAATAATTAAGGAAATAAATTAAATCCAGGTTTAACCC
          1 CCTAATAATCAAGGAAAGAAATTAAATCCAGGTTTAACCC

                          *                     *   
       5705 CCTAATAATCAAGGTAAGAAATTAAATCCAGGTTTAGCCC
          1 CCTAATAATCAAGGAAAGAAATTAAATCCAGGTTTAACCC

             
       5745 C
          1 C

       5746 TAGTTATAAA


Statistics
Matches: 37,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  40   37  1.00

ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26


Consensus pattern (40 bp):   
CCTAATAATCAAGGAAAGAAATTAAATCCAGGTTTAACCC

Found at i:12805 original size:15 final size:15

Alignment explanation


    Indices: 12787--12847  Score: 104
    Period size: 15  Copynumber: 4.1  Consensus size: 15

      12777 CATTTATTTG

                           
      12787 GTATTCAGCATTTTA
          1 GTATTCAGCATTTTA

                           
      12802 GTATTCAGCATTTTA
          1 GTATTCAGCATTTTA

                   *       
      12817 GTATTCAACATTTTA
          1 GTATTCAGCATTTTA

                    *      
      12832 GTATTCAGAATTTTA
          1 GTATTCAGCATTTTA

             
      12847 G
          1 G

      12848 GTTTCAAAGG


Statistics
Matches: 43,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   43  1.00

ACGTcount: A:0.30, C:0.11, G:0.13, T:0.46


Consensus pattern (15 bp):   
GTATTCAGCATTTTA

Found at i:18890 original size:69 final size:69

Alignment explanation


    Indices: 18776--18990  Score: 340
    Period size: 69  Copynumber: 3.1  Consensus size: 69

      18766 AAGTCCTGTA

                  *           **      *                                      
      18776 GACTTGGGCTGTTGAGGAATGCAAAAATACAGGACAAGACCTGGGCAGGAGTTACCCAAGTCCTG
          1 GACTTGTGCTGTTGAGGAGCGC-AAATTACAGGACAAGACCTGGGCAGGAGTTACCCAAGTCCTG

                 
      18841 TCCCG
         65 TCCCG

                           *                             *                   
      18846 GACTTGTGCTGTTGAAGAGCGCAAATTACAGGACAAGACCTGGGCGGGAGTTACCCAAGTCCTGT
          1 GACTTGTGCTGTTGAGGAGCGCAAATTACAGGACAAGACCTGGGCAGGAGTTACCCAAGTCCTGT

                
      18911 CCCG
         66 CCCG

                                                                         *   
      18915 GACTTGTGCTGTTGAGGAGCGCAAATTACAGGACAAGACCTGGGCAGGAGTTACCCAAGTCTTGT
          1 GACTTGTGCTGTTGAGGAGCGCAAATTACAGGACAAGACCTGGGCAGGAGTTACCCAAGTCCTGT

              * 
      18980 CCAG
         66 CCCG

              *    
      18984 GAGTTGT
          1 GACTTGT

      18991 TGCGGGAAAT


Statistics
Matches: 134,  Mismatches: 11, Indels: 1
        0.92            0.08        0.01

Matches are distributed among these distances:
  69  116  0.87
  70   18  0.13

ACGTcount: A:0.26, C:0.22, G:0.31, T:0.21


Consensus pattern (69 bp):   
GACTTGTGCTGTTGAGGAGCGCAAATTACAGGACAAGACCTGGGCAGGAGTTACCCAAGTCCTGT
CCCG
Done.