Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017262.1 Corchorus olitorius cultivar O-4 contig17295, 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: 7754
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:2643 original size:19 final size:18

Alignment explanation


    Indices: 2610--2645  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       2600 TTGAAATAAT

                              
       2610 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
       2628 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

       2646 TGAGTCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA

Found at i:2653 original size:11 final size:10

Alignment explanation


    Indices: 2610--2657  Score: 55
    Period size: 11  Copynumber: 4.8  Consensus size: 10

       2600 TTGAAATAAT

                      
       2610 TCTTCAATGA
          1 TCTTCAATGA

                      
       2620 TCTTCAA--A
          1 TCTTCAATGA

                     * 
       2628 TCTTCAAATTA
          1 TCTTC-AATGA

                      
       2639 TCTTCAATGA
          1 TCTTCAATGA

                     
       2649 GTCTTCAAT
          1 -TCTTCAAT

       2658 CACGAGCTTC


Statistics
Matches: 33,  Mismatches: 1, Indels: 7
        0.80            0.02        0.17

Matches are distributed among these distances:
   8    6  0.18
   9    2  0.06
  10   11  0.33
  11   14  0.42

ACGTcount: A:0.31, C:0.21, G:0.06, T:0.42


Consensus pattern (10 bp):   
TCTTCAATGA

Found at i:5655 original size:33 final size:33

Alignment explanation


    Indices: 5601--5699  Score: 153
    Period size: 33  Copynumber: 3.0  Consensus size: 33

       5591 CAGGGAAGCA

                  *                         * 
       5601 GCCCCGCGCTTGGCACGCGGGCTGGCCTGGTGGT
          1 GCCCCGTGC-TGGCACGCGGGCTGGCCTGGTGAT

                        *                    
       5635 GCCCCGTGCTGGAACGCGGGCTGGCCTGGTGAT
          1 GCCCCGTGCTGGCACGCGGGCTGGCCTGGTGAT

                         *                  
       5668 GCCCCGTGCTGGCGCGCGGGCTGGCCTGGTGA
          1 GCCCCGTGCTGGCACGCGGGCTGGCCTGGTGA

       5700 CCGAGTCATG


Statistics
Matches: 60,  Mismatches: 5, Indels: 1
        0.91            0.08        0.02

Matches are distributed among these distances:
  33   52  0.87
  34    8  0.13

ACGTcount: A:0.05, C:0.33, G:0.44, T:0.17


Consensus pattern (33 bp):   
GCCCCGTGCTGGCACGCGGGCTGGCCTGGTGAT
Done.