Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016247.1 Corchorus olitorius cultivar O-4 contig16280, 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: 50255
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30


Found at i:6112 original size:15 final size:15

Alignment explanation


    Indices: 6094--6146  Score: 52
    Period size: 15  Copynumber: 3.3  Consensus size: 15

       6084 TTAAAATTAA

                 *         
       6094 TTATTCTTAATTAGT
          1 TTATTATTAATTAGT

                        *     
       6109 TTATTAGTTTGACTTAGT
          1 TTATTA--TT-AATTAGT

                *          
       6127 TTATAATTAATTAGT
          1 TTATTATTAATTAGT

                 
       6142 TTATT
          1 TTATT

       6147 TACGATTAAT


Statistics
Matches: 30,  Mismatches: 5, Indels: 6
        0.73            0.12        0.15

Matches are distributed among these distances:
  15   15  0.50
  16    2  0.07
  17    2  0.07
  18   11  0.37

ACGTcount: A:0.28, C:0.04, G:0.09, T:0.58


Consensus pattern (15 bp):   
TTATTATTAATTAGT

Found at i:9946 original size:15 final size:15

Alignment explanation


    Indices: 9926--9955  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       9916 TCGCATATTG

                  *        
       9926 TTCGTCCACGCATGA
          1 TTCGTCAACGCATGA

                           
       9941 TTCGTCAACGCATGA
          1 TTCGTCAACGCATGA

       9956 ACGAACTTCT


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27


Consensus pattern (15 bp):   
TTCGTCAACGCATGA

Found at i:25483 original size:15 final size:15

Alignment explanation


    Indices: 25436--25474  Score: 53
    Period size: 15  Copynumber: 2.7  Consensus size: 15

      25426 AACCTGAAGT

                         * 
      25436 CGCC-CCTCCTCCCC
          1 CGCCACCTCCTCCAC

                 *         
      25450 CGCCAGCTCCTCCAC
          1 CGCCACCTCCTCCAC

                      
      25465 CGCCACCTCC
          1 CGCCACCTCC

      25475 ACCGCCGCCC


Statistics
Matches: 21,  Mismatches: 3, Indels: 1
        0.84            0.12        0.04

Matches are distributed among these distances:
  14    4  0.19
  15   17  0.81

ACGTcount: A:0.08, C:0.69, G:0.10, T:0.13


Consensus pattern (15 bp):   
CGCCACCTCCTCCAC

Found at i:46112 original size:15 final size:15

Alignment explanation


    Indices: 46092--46123  Score: 55
    Period size: 15  Copynumber: 2.1  Consensus size: 15

      46082 CCTATAGGGC

                     *     
      46092 TTTATTTGAGCAATT
          1 TTTATTTGAACAATT

                           
      46107 TTTATTTGAACAATT
          1 TTTATTTGAACAATT

              
      46122 TT
          1 TT

      46124 CACAACATTA


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.28, C:0.06, G:0.09, T:0.56


Consensus pattern (15 bp):   
TTTATTTGAACAATT
Done.