Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009851.1 Corchorus olitorius cultivar O-4 contig09883, 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: 5810
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34


Found at i:842 original size:15 final size:14

Alignment explanation


    Indices: 822--851  Score: 51
    Period size: 15  Copynumber: 2.1  Consensus size: 14

        812 AATTTTCAAA

                           
        822 TAAAATAAAATATAT
          1 TAAAATAAAA-ATAT

                          
        837 TAAAATAAAAATAT
          1 TAAAATAAAAATAT

             
        851 T
          1 T

        852 TATTTTTATT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    5  0.33
  15   10  0.67

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (14 bp):   
TAAAATAAAAATAT

Found at i:4189 original size:25 final size:25

Alignment explanation


    Indices: 4160--4221  Score: 97
    Period size: 25  Copynumber: 2.5  Consensus size: 25

       4150 CAATTAGTAC

                                     
       4160 TCTACATATTTTGAATGTCATTCTT
          1 TCTACATATTTTGAATGTCATTCTT

                                  *  
       4185 TCTACATATTTTGAATGTCATTTTT
          1 TCTACATATTTTGAATGTCATTCTT

               *   *    
       4210 TCTTCATCTTTT
          1 TCTACATATTTT

       4222 TTTTTTTGGC


Statistics
Matches: 34,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  25   34  1.00

ACGTcount: A:0.21, C:0.16, G:0.06, T:0.56


Consensus pattern (25 bp):   
TCTACATATTTTGAATGTCATTCTT

Found at i:5558 original size:2 final size:2

Alignment explanation


    Indices: 5551--5590  Score: 80
    Period size: 2  Copynumber: 20.0  Consensus size: 2

       5541 TCCTCAGGGA

                                                                       
       5551 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       5591 TGTCACCTTC


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   38  1.00

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


Consensus pattern (2 bp):   
AT

Done.