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Title:
 
2008-12-30 22:09:52
Mirai_18684 - hemoglobin
Type notes here
Tool: Primer_Blast_results
2008-12-30 22:11:10
Result sets:  1Need help?

Mirai_18684 - hemoglobin

Input PCR template
 
Range
1 - 564
Specificity of primers
Primer pairs are specific to input template as no other targets were found in selected database: NCBI Transcript Reference Sequences (Organism limited to Homo sapiens)
Summary of primer pairs

Detailed primer reports

Primer pair 1

Sequence (5'->3')Strand on templateLengthStartStopTmGC%
Forward primerAGAACTGCTGGGGGAAGATTPlus20517060.0750.00%
Reverse primerCGGCTTAACGGTACTTGGAGMinus2044943059.7655.00%
Product length399

Primer pair 2

Sequence (5'->3')Strand on templateLengthStartStopTmGC%
Forward primerAGAACTGCTGGGGGAAGATTPlus20517060.0750.00%
Reverse primerGGCAAGGAATTTGTCCAGAGMinus2040939059.6750.00%
Product length359

Primer pair 3

Sequence (5'->3')Strand on templateLengthStartStopTmGC%
Forward primerAGAACTGCTGGGGGAAGATTPlus20517060.0750.00%
Reverse primerAGGCAAGGAATTTGTCCAGAMinus2041039159.6745.00%
Product length360

Primer pair 4

Sequence (5'->3')Strand on templateLengthStartStopTmGC%
Forward primerAGAACTGCTGGGGGAAGATTPlus20517060.0750.00%
Reverse primerGAGGCAAGGAATTTGTCCAGMinus2041139259.6750.00%
Product length361

Primer pair 5

Sequence (5'->3')Strand on templateLengthStartStopTmGC%
Forward primerAGAACTGCTGGGGGAAGATTPlus20517060.0750.00%
Reverse primerTGTGAAATCTCCAGGGTGGTMinus2037335460.3650.00%
Product length323

Primer pair 6

Sequence (5'->3')Strand on templateLengthStartStopTmGC%
Forward primerAGAACTGCTGGGGGAAGATTPlus20517060.0750.00%
Reverse primerGTGTGAAATCTCCAGGGTGGMinus2037435560.3655.00%
Product length324

Primer pair 7

Sequence (5'->3')Strand on templateLengthStartStopTmGC%
Forward primerAGAACTGCTGGGGGAAGATTPlus20517060.0750.00%
Reverse primerGGTGTGAAATCTCCAGGGTGMinus2037535660.3655.00%
Product length325

Primer pair 8

Sequence (5'->3')Strand on templateLengthStartStopTmGC%
Forward primerAGAACTGCTGGGGGAAGATTPlus20517060.0750.00%
Reverse primerACAGGATCCACACGCAGTTTMinus2030628760.5850.00%
Product length256

Primer pair 9

Sequence (5'->3')Strand on templateLengthStartStopTmGC%
Forward primerAGAACTGCTGGGGGAAGATTPlus20517060.0750.00%
Reverse primerAGGATCCACACGCAGTTTGTMinus2030428560.5850.00%
Product length254

Primer pair 10

Sequence (5'->3')Strand on templateLengthStartStopTmGC%
Forward primerAGAACTGCTGGGGGAAGATTPlus20517060.0750.00%
Reverse primerAGGTCGCTCAGAGTGGACAGMinus2027625760.6160.00%
Product length226
 
2008-12-30 22:12:28
Mirai_18685 - not defined
Mirai_18686 - not defined
Type notes here
Tool: IDT_Oligo_Analyzer_results
2008-12-30 22:12:32
Result pages:1 | 2Need help?

Mirai_18685 - not defined

Sequence 5' -> 3':

AGA ACT GCT GGG GGA AGA TT

RESULTS
SEQUENCE:
5'- AGA ACT GCT GGG GGA AGA TT -3'
COMPLEMENT:
5'- AAT CTT CCC CCA GCA GTT CT -3'
LENGTH: 20
GC CONTENT: 50 %
MELT TEMP: 56.2 ºC
MOLECULAR
WEIGHT:		 6246.1 g/mole
EXTINCTION
COEFFICIENT:		 203700 L/(mole·cm)
nmole/OD260: 4.91
ug/OD260: 30.66

MELTING TEMPERATURE SETTINGS
TARGET TYPE: DNA
OLIGO CONC 0.25 µM
Na+ CONC 50 mM monovalent salt



MELTING TEMPERATURE ASSUMPTIONS AND LIMITATIONS
  • Predictions are accurate for oligos from 8 to 60 bases in length, in neutral buffered solutions (pH 7 - 8) with monovalent cation concentrations from 10mM to 1.2 M.

  • Oligo concentration is assumed to be significantly larger (at least 6x) than concentration of the complementary target, which is true in majority of molecular biology experiments. If this is not a case, concentration of the target cannot be ignored and you should enter in the box,

    Oligo Conc = [strand1] – [strand2]/2 when [strand1] ≥ [strand2]
    Oligo Conc = ([strand1] + [strand2])/4 when [strand1] = [strand2]


  • Melting temperature accuracy and models: (Oligo/Template)


    • DNA/DNA: +/- 1.4ºC (Allawi '97)
    LNA/DNA: +/- 2.0ºC (McTigue '04)
    RNA/DNA: +/- 2.7ºC (Sugimoto '95)
    DNA/RNA: +/- 2.7ºC (Sugimoto '95)
    RNA/RNA: +/- 1.3ºC (Xia '98)
    Monovalent cation correction: +/- 2.0ºC (Owczarzy '04)

  • Non-consecutive LNA bases hybridized to a DNA template use a model from McTigue '04. Consecutive LNA bases on a DNA template and any LNA bases on an RNA template assume RNA energetic parameters and predictions are therefore less accurate.

  • Effects of chemical modifications are neglected except when the modification contains a base, e.g., 5-Methyl dC, Internal Fluorescein dT. Energetic effects of these modifications are only approximated.

  • This OligoAnalyzer version does not account for effects of divalent cations.

HOMO-DIMER ANALYSIS

Dimer Sequence 
5'- AGAACTGCTGGGGGAAGATT -3'
Maximum Delta G -39.09 kcal/mole


Delta G: -3.14 kcal/mole
Base Pairs: 2
5'       AGAACTGCTGGGGGAAGATT
             : || :          
3' TTAGAAGGGGGTCGTCAAGA


Delta G: -1.94 kcal/mole
Base Pairs: 2
5' AGAACTGCTGGGGGAAGATT
     ||              ::  
3'   TTAGAAGGGGGTCGTCAAGA


Delta G: -1.94 kcal/mole
Base Pairs: 2
5' AGAACTGCTGGGGGAAGATT
                 ||  ::              
3'               TTAGAAGGGGGTCGTCAAGA


Delta G: -1.6 kcal/mole
Base Pairs: 2
5'               AGAACTGCTGGGGGAAGATT
                 ||  ::              
3' TTAGAAGGGGGTCGTCAAGA


Delta G: -1.6 kcal/mole
Base Pairs: 2
5'            AGAACTGCTGGGGGAAGATT
              || : : ::           
3' TTAGAAGGGGGTCGTCAAGA


Delta G: -1.6 kcal/mole
Base Pairs: 2
5' AGAACTGCTGGGGGAAGATT
     : || :     : :: :  
3'  TTAGAAGGGGGTCGTCAAGA


Delta G: -1.6 kcal/mole
Base Pairs: 2
5' AGAACTGCTGGGGGAAGATT
          ||      ::       
3'     TTAGAAGGGGGTCGTCAAGA


Delta G: -1.47 kcal/mole
Base Pairs: 2
5' AGAACTGCTGGGGGAAGATT
                    ||                 
3'                 TTAGAAGGGGGTCGTCAAGA


IDT Oligo Analyzer results from DNASIS SmartNote