TugasKu: Design Primer (Bioinformatika)

TUGAS BIOINFORMATIKA

DESIGN PRIMER

              Nama      : Diana Putri Hapsari

              NIM       : M041018

JURUSAN BIOLOGI

FAKULTAS MATEMATIKA DAN ILMU PENGETAHUAN ALAM

UNIVERSITAS SEBELAS MARET

SURAKARTA

2012

Saccharomyces cerevisiae

NC_001139

Primer3 Output:

No mispriming library specified

Using 1-based sequence positions

OLIGO                     start  len      tm     gc%   any    3' seq

LEFT PRIMER        120   20   57.98   45.00  3.00  2.00 TTTACAAGCCGTTACCAAGC

RIGHT PRIMER      1240   20   58.06   50.00  8.00  0.00 TGTGACCGGTCTTGTAACCT

SEQUENCE SIZE: 1461

INCLUDED REGION SIZE: 1461

ADDITIONAL OLIGOS

                                     start  len      tm     gc%   any    3' seq

 1 LEFT PRIMER        166   20   58.05   45.00  4.00  1.00 TTGTCCAAGAAGGGTGGTAA

   RIGHT PRIMER      1240   20   58.06   50.00  8.00  0.00 TGTGACCGGTCTTGTAACCT

   PRODUCT SIZE: 1075, PAIR ANY COMPL: 6.00, PAIR 3' COMPL: 2.00

 2 LEFT PRIMER        165   20   58.05   45.00  4.00  2.00 TTTGTCCAAGAAGGGTGGTA

   RIGHT PRIMER      1240   20   58.06   50.00  8.00  0.00 TGTGACCGGTCTTGTAACCT

   PRODUCT SIZE: 1076, PAIR ANY COMPL: 6.00, PAIR 3' COMPL: 1.00

 3 LEFT PRIMER        159   20   58.15   45.00  4.00  0.00 AAAGGGTTTGTCCAAGAAGG

   RIGHT PRIMER      1240   20   58.06   50.00  8.00  0.00 TGTGACCGGTCTTGTAACCT

   PRODUCT SIZE: 1082, PAIR ANY COMPL: 5.00, PAIR 3' COMPL: 3.00

 4 LEFT PRIMER        226   20   57.85   45.00  5.00  3.00 GGTAAGGAATCCGGTGATTT

   RIGHT PRIMER      1240   20   58.06   50.00  8.00  0.00 TGTGACCGGTCTTGTAACCT

   PRODUCT SIZE: 1015, PAIR ANY COMPL: 5.00, PAIR 3' COMPL: 1.00

Output FastPCR:

_______________________________

In silico Primer(s) search for: 1

primer forward  5'-tttacaagccgttaccaagc

Position: 120->139   20bp   100%   Tm = 52,7°C

5-tttacaagccgttaccaagc->

  |||||||||||||||||||| 

actttacaagccgttaccaagcactt

primer reverse (reverse complement)  5'-tgtgaccggtcttgtaacct

Position: 1221<-1240 20bp   100%   Tm = 55,2°C

<-tccaatgttctggccagtgt-5

  |||||||||||||||||||| 

agaggttacaagaccggtcacatc

primer forward  5'-tttacaagccgttaccaagc

primer reverse (reverse complement)  5'-tgtgaccggtcttgtaacct

 PCR product size: 1121bp  Ta=61°C

DNA Calculator Primer Forward:

Minimum base pairs required for single primer self-dimerization: 5.

Minimum base pairs required for a hairpin: 4.

Sorry, the hairpin loop calculation is only available if you are using Netscape or IE 4.0 or higher!

3' Complementarity:

 None !

All potential self-annealing sites are marked in red (allowing 1 mis-match):

 None !

DNA Calculator Primer Reverse:

Minimum base pairs required for single primer self-dimerization: 5.

Minimum base pairs required for a hairpin: 4.

Sorry, the hairpin loop calculation is only available if you are using Netscape or IE 4.0 or higher!

3' Complementarity:

 None !

All potential self-annealing sites are marked in red (allowing 1 mis-match):

 None !