Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016182.1 Corchorus olitorius cultivar O-4 contig16215, 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: 14517
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:3668 original size:20 final size:20

Alignment explanation


    Indices: 3643--3683  Score: 73
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       3633 CGTCATTTGG

                       *        
       3643 TCTTTTAGCCATGTGTCACT
          1 TCTTTTAGCCACGTGTCACT

                                
       3663 TCTTTTAGCCACGTGTCACT
          1 TCTTTTAGCCACGTGTCACT

             
       3683 T
          1 T

       3684 TCACTCTCCC


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.15, C:0.27, G:0.15, T:0.44


Consensus pattern (20 bp):   
TCTTTTAGCCACGTGTCACT

Found at i:4960 original size:2 final size:2

Alignment explanation


    Indices: 4955--4991  Score: 74
    Period size: 2  Copynumber: 18.5  Consensus size: 2

       4945 GTCTTCTCTC

                                                                   
       4955 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       4992 ATTGATTGAA


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   35  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:9460 original size:14 final size:14

Alignment explanation


    Indices: 9441--9468  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

       9431 CAAAACCAAC

                          
       9441 TCCTCTGTTTTTAT
          1 TCCTCTGTTTTTAT

                          
       9455 TCCTCTGTTTTTAT
          1 TCCTCTGTTTTTAT

       9469 GACTTCTCTG


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.07, C:0.21, G:0.07, T:0.64


Consensus pattern (14 bp):   
TCCTCTGTTTTTAT

Found at i:14330 original size:18 final size:19

Alignment explanation


    Indices: 14291--14330  Score: 55
    Period size: 21  Copynumber: 2.1  Consensus size: 19

      14281 GTGCTCCCGT

                                 
      14291 TGTGATGCTCCCACTTTTCAA
          1 TGTGATGCTCCCA--TTTCAA

                               
      14312 TGTGATGCTCCCA-TTCAA
          1 TGTGATGCTCCCATTTCAA

             
      14330 T
          1 T

      14331 TCTGACCATT


Statistics
Matches: 19,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  18    6  0.32
  21   13  0.68

ACGTcount: A:0.20, C:0.28, G:0.15, T:0.38


Consensus pattern (19 bp):   
TGTGATGCTCCCATTTCAA
Done.