Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015218.1 Corchorus olitorius cultivar O-4 contig15251, 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: 12367
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31


Found at i:11879 original size:39 final size:39

Alignment explanation


    Indices: 11817--11931  Score: 135
    Period size: 39  Copynumber: 3.0  Consensus size: 39

      11807 AACACACAAG

                               *                    
      11817 AATCA-TTTTTTTTGGATAATTTTGGTTGAATCTGGTAAA
          1 AATCACTTTTTTTTGG-TATTTTTGGTTGAATCTGGTAAA

                                                  *
      11856 AATCACTTTTTTTTGGTATTTTTGGTTGAATCTGGTAAG
          1 AATCACTTTTTTTTGGTATTTTTGGTTGAATCTGGTAAA

            *  *    **      *              *      
      11895 TATGAC-TAGTTTTGGGATTTTTGGTTGAATATGGTAA
          1 AATCACTTTTTTTTGGTATTTTTGGTTGAATCTGGTAA

      11932 GTATGACTAG


Statistics
Matches: 67,  Mismatches: 8, Indels: 3
        0.86            0.10        0.04

Matches are distributed among these distances:
  38   27  0.40
  39   30  0.45
  40   10  0.15

ACGTcount: A:0.24, C:0.05, G:0.22, T:0.49


Consensus pattern (39 bp):   
AATCACTTTTTTTTGGTATTTTTGGTTGAATCTGGTAAA

Found at i:11908 original size:38 final size:38

Alignment explanation


    Indices: 11826--11947  Score: 154
    Period size: 38  Copynumber: 3.2  Consensus size: 38

      11816 GAATCATTTT

                     *                   **  *    **
      11826 TTTTGGATAATTTTGGTTGAATCTGGTAAAAATCACTTTT
          1 TTTTGG-TATTTTTGGTTGAATCTGGTAAGTATGAC-TAG

                                                  
      11866 TTTTGGTATTTTTGGTTGAATCTGGTAAGTATGACTAG
          1 TTTTGGTATTTTTGGTTGAATCTGGTAAGTATGACTAG

                  *              *                
      11904 TTTTGGGATTTTTGGTTGAATATGGTAAGTATGACTAG
          1 TTTTGGTATTTTTGGTTGAATCTGGTAAGTATGACTAG

                  
      11942 TTTTGG
          1 TTTTGG

      11948 GAAGGAGAGC


Statistics
Matches: 74,  Mismatches: 8, Indels: 2
        0.88            0.10        0.02

Matches are distributed among these distances:
  38   43  0.58
  39   25  0.34
  40    6  0.08

ACGTcount: A:0.23, C:0.05, G:0.25, T:0.48


Consensus pattern (38 bp):   
TTTTGGTATTTTTGGTTGAATCTGGTAAGTATGACTAG

Done.