Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023994.1 Corchorus olitorius cultivar O-4 contig24027, 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: 21860
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:18 original size:2 final size:2

Alignment explanation


    Indices: 6--41  Score: 63
    Period size: 2  Copynumber: 17.5  Consensus size: 2

          1 TTTAT

                                                                 
          6 TA TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

         42 GGGCATATGA


Statistics
Matches: 33,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   2   31  0.94
   3    2  0.06

ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:2838 original size:11 final size:11

Alignment explanation


    Indices: 2822--2851  Score: 60
    Period size: 11  Copynumber: 2.7  Consensus size: 11

       2812 CTGAATCTGA

                       
       2822 TTTGTTTTTTT
          1 TTTGTTTTTTT

                       
       2833 TTTGTTTTTTT
          1 TTTGTTTTTTT

                    
       2844 TTTGTTTT
          1 TTTGTTTT

       2852 ACTTTGTTAC


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   19  1.00

ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90


Consensus pattern (11 bp):   
TTTGTTTTTTT

Found at i:7698 original size:48 final size:48

Alignment explanation


    Indices: 7631--7730  Score: 182
    Period size: 48  Copynumber: 2.1  Consensus size: 48

       7621 AACCCTTATA

                                 *                          
       7631 TTTTTCACCTCAAACAATTTGGCACGCCTGGTGGGACACTAGGGATTT
          1 TTTTTCACCTCAAACAATTTGACACGCCTGGTGGGACACTAGGGATTT

                                                  *         
       7679 TTTTTCACCTCAAACAATTTGACACGCCTGGTGGGACATTAGGGATTT
          1 TTTTTCACCTCAAACAATTTGACACGCCTGGTGGGACACTAGGGATTT

                
       7727 TTTT
          1 TTTT

       7731 CAAATCATGC


Statistics
Matches: 50,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  48   50  1.00

ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35


Consensus pattern (48 bp):   
TTTTTCACCTCAAACAATTTGACACGCCTGGTGGGACACTAGGGATTT
Done.