Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01004225.1 Corchorus olitorius cultivar O-4 contig04238, 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, 802

Length: 1338
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.22


Found at i:136 original size:21 final size:21

Alignment explanation


    Indices: 28--136  Score: 52
    Period size: 21  Copynumber: 5.2  Consensus size: 21

         18 CGTTGACAGC

                                 
         28 CTGAAGAGTGATGTCAGCGTA
          1 CTGAAGAGTGATGTCAGCGTA

                         *       ***
         49 CTG-AGAACG-GACGTC-GACACC
          1 CTGAAG-A-GTGATGTCAG-CGTA

                                 
         70 CTGAAGAGTGATGTCAGCGTA
          1 CTGAAGAGTGATGTCAGCGTA

                         *          *
         91 CTG-AGAACG-GACGTC-GACAG-C
          1 CTGAAG-A-GTGATGTCAG-C-GTA

                                 
        112 CTGAAGAGTGATGTCAGCGTA
          1 CTGAAGAGTGATGTCAGCGTA

                
        133 CTGA
          1 CTGA

        137 GAACGGACGT


Statistics
Matches: 62,  Mismatches: 12, Indels: 28
        0.61            0.12        0.27

Matches are distributed among these distances:
  20    9  0.15
  21   44  0.71
  22    9  0.15

ACGTcount: A:0.28, C:0.21, G:0.32, T:0.18


Consensus pattern (21 bp):   
CTGAAGAGTGATGTCAGCGTA

Found at i:209 original size:42 final size:42

Alignment explanation


    Indices: 1--200  Score: 319
    Period size: 42  Copynumber: 4.8  Consensus size: 42

                 *        *                           
          1 AGCGTGCTGAGAACAGACGTTGACAGCCTGAAGAGTGATGTC
          1 AGCGTACTGAGAACGGACGTTGACAGCCTGAAGAGTGATGTC

                                *    *                
         43 AGCGTACTGAGAACGGACGTCGACACCCTGAAGAGTGATGTC
          1 AGCGTACTGAGAACGGACGTTGACAGCCTGAAGAGTGATGTC

                                *                     
         85 AGCGTACTGAGAACGGACGTCGACAGCCTGAAGAGTGATGTC
          1 AGCGTACTGAGAACGGACGTTGACAGCCTGAAGAGTGATGTC

                                                      
        127 AGCGTACTGAGAACGGACGTTGACAGCCTGAAGAGTGATGTC
          1 AGCGTACTGAGAACGGACGTTGACAGCCTGAAGAGTGATGTC

                 *        *      * *        
        169 AGCGTGCTGAGAACAGACGTTAATAGCCTGAA
          1 AGCGTACTGAGAACGGACGTTGACAGCCTGAA

        201 AACCGATGTG


Statistics
Matches: 148,  Mismatches: 10, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  42  148  1.00

ACGTcount: A:0.29, C:0.20, G:0.32, T:0.18


Consensus pattern (42 bp):   
AGCGTACTGAGAACGGACGTTGACAGCCTGAAGAGTGATGTC

Done.