Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013231.1 Corchorus olitorius cultivar O-4 contig13264, 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: 7745
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37


Found at i:380 original size:19 final size:18

Alignment explanation


    Indices: 351--386  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

        341 ATCTAACTTA

                              
        351 TTTTTATTTTTATTTTAG
          1 TTTTTATTTTTATTTTAG

                        *     
        369 TTTTTATGTTTTCTTTTA
          1 TTTTTAT-TTTTATTTTA

        387 ATTTAATTCT


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

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.14, C:0.03, G:0.06, T:0.78


Consensus pattern (18 bp):   
TTTTTATTTTTATTTTAG

Found at i:3569 original size:2 final size:2

Alignment explanation


    Indices: 3562--3596  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       3552 ACAATTCATG

                                                                
       3562 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
          1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C

       3597 AATATAAAAG


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49


Consensus pattern (2 bp):   
CT

Found at i:7405 original size:25 final size:24

Alignment explanation


    Indices: 7355--7406  Score: 68
    Period size: 25  Copynumber: 2.1  Consensus size: 24

       7345 CCTTGAATTT

                          *      *  
       7355 TTTAATGTTTAATTCTTAAATTTA
          1 TTTAATGTTTAATTATTAAATCTA

                              *      
       7379 TTTAATGTCTTAATTATTCAATCTA
          1 TTTAATGT-TTAATTATTAAATCTA

               
       7404 TTT
          1 TTT

       7407 TACAATCCAC


Statistics
Matches: 24,  Mismatches: 3, Indels: 1
        0.86            0.11        0.04

Matches are distributed among these distances:
  24    8  0.33
  25   16  0.67

ACGTcount: A:0.31, C:0.08, G:0.04, T:0.58


Consensus pattern (24 bp):   
TTTAATGTTTAATTATTAAATCTA
Done.