Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023074.1 Corchorus olitorius cultivar O-4 contig23107, 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: 9507
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34


Found at i:17 original size:2 final size:2

Alignment explanation


    Indices: 11--41  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

          1 TAATATTTAG

                                                          
         11 TA TA 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 T

         42 TCTTTTTGTT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:1848 original size:47 final size:47

Alignment explanation


    Indices: 1782--1944  Score: 299
    Period size: 47  Copynumber: 3.5  Consensus size: 47

       1772 TTGACTCCTC

                          *                                
       1782 TTTATTACTTAGTTTAATTACCTAGAATTAAATTAATTTCTTCTTCT
          1 TTTATTACTTAGTTCAATTACCTAGAATTAAATTAATTTCTTCTTCT

                                                           
       1829 TTTATTACTTAGTTCAATTACCTAGAATTAAATTAATTTCTTCTTCT
          1 TTTATTACTTAGTTCAATTACCTAGAATTAAATTAATTTCTTCTTCT

                                       *                   
       1876 TTTATTACTTAGTTCAATTACCTAGAAATAAATTAATTTCTTCTTCT
          1 TTTATTACTTAGTTCAATTACCTAGAATTAAATTAATTTCTTCTTCT

                             *    
       1923 TTTATTACTTAGTTCAAATACC
          1 TTTATTACTTAGTTCAATTACC

       1945 CACTGTAAAC


Statistics
Matches: 113,  Mismatches: 3, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  47  113  1.00

ACGTcount: A:0.31, C:0.15, G:0.04, T:0.50


Consensus pattern (47 bp):   
TTTATTACTTAGTTCAATTACCTAGAATTAAATTAATTTCTTCTTCT

Found at i:4828 original size:26 final size:26

Alignment explanation


    Indices: 4769--4861  Score: 159
    Period size: 26  Copynumber: 3.5  Consensus size: 26

       4759 ACAATAATTT

                              * *      
       4769 TGACCAAAATGCCCCTGAAGTGAAAAA
          1 TGACCAAAATGCCCCTGAGGCG-AAAA

                                      
       4796 TGACCAAAATGCCCCTGAGGCGAAAA
          1 TGACCAAAATGCCCCTGAGGCGAAAA

                                      
       4822 TGACCAAAATGCCCCTGAGGCGAAAA
          1 TGACCAAAATGCCCCTGAGGCGAAAA

                          
       4848 TGACCAAAATGCCC
          1 TGACCAAAATGCCC

       4862 ATGGTGAATT


Statistics
Matches: 64,  Mismatches: 2, Indels: 1
        0.96            0.03        0.01

Matches are distributed among these distances:
  26   44  0.69
  27   20  0.31

ACGTcount: A:0.40, C:0.27, G:0.20, T:0.13


Consensus pattern (26 bp):   
TGACCAAAATGCCCCTGAGGCGAAAA
Done.