8/13/2019 Primer NDV B1

1/4

Primer-BLAST Primer-Blast results

NCBI/ Primer-BLAST: results: Job id=JSID_01_183233_130.14.22.21_9002_primertool more...

Input PCR template

Range

1 - 1782

Specificity of primers

primer specificity was not determined as specificity checking option was not selected.Other reports

Search Summary

Search parameters and other details

Search parameter name Search parameter value

Number of Blast hits analyzed 0

Entrez query

Min total mismatches 2

Min 3' end mismatches 2

Defined 3' end region length 5

Mismatch threshold to ignore targets 6

Misprimed product size deviation 4000

Max number of Blast target sequences50000Blast E value 30000

Blast word size 7

Max candidate primer pairs 500

Min PCR product size 70

Max PCR product size 200

Min Primer size 15

Opt Primer size 20

Max Primer size 25

Min Tm 57

Opt Tm 60

Max Tm 63Max Tm difference 3

Repeat filter AUTO

Low complexity filter Yes

Graphical view of primer pairs

Detailed primer reports

Primer pair 1

Sequence (5'->3') Template

LengthStart StopTm GC%Self Self 3'

Pr i mer pai r s f or submi t t ed sequence

er-Blast results http://www.ncbi.nlm.nih.gov/tools/primer-blast/prim

1/17/2014

8/13/2019 Primer NDV B1

2/4

strand complementarity complementarity

Forward

primerCTGCCAACATCCTCCGACTT Plus 20 489 508 60.04 55.00 3.00 0.00

Reverse

primerCTTCCCAACTGCCACTGCTA Minus 20 589 570 59.96 55.00 3.00 2.00

Internal

oligoPlus

Product

length101

Product Tm

Product Tm

- min(OLIGO

Tm)

Exon

junction

Total intron

size

Products on intended target

Products on allowed transcript variants

Products on potentially unintended templates

Products on target templates

Primer pair 2

Sequence (5'->3') Template

strand LengthStart StopTm GC%

Self

complementarity

Self 3'

complementarity

Forward

primerTTATTGGCGGTGTGGCTCTT Plus 20 408 427 59.9650.002.00 0.00

Reverse

primerAAGTCGGAGGATGTTGGCAGMinus 20 508 489 60.0455.00 3.00 1.00

Internal

oligoPlus

Product

length101

Product Tm

Product Tm

-

min(OLIGO

Tm)

Exon

junction

Total intron

size

Products on intended target

Products on allowed transcript variants

Products on potentially unintended templates

Products on target templates

Primer pair 3

Sequence (5'->3') Template

strand LengthStart StopTm GC%

Self

complementarity

Self 3'

complementarity

er-Blast results http://www.ncbi.nlm.nih.gov/tools/primer-blast/prim

1/17/2014

8/13/2019 Primer NDV B1

3/4

Forward

primerTCGGTAGCGGCTTAATCACC Plus 20 837 856 59.90 55.00 5.00 2.00

Reverse

primerCACTTTTGGGACAAGTGCCG Minus 20 1012 993 59.97 55.00 7.00 2.00

Internal

oligoPlus

Product

length176

Product Tm

Product Tm

-

min(OLIGO

Tm)

Exon

junction

Total intron

size

Products on intended target

Products on allowed transcript variants

Products on potentially unintended templates

Products on target templates

Primer pair 4

Sequence (5'->3') Template

strand LengthStart StopTm GC%

Self

complementarity

Self 3'

complementarity

Forward

primerATCCGTAAGCACAACCAGGG Plus 20 964 983 60.04 55.00 3.00 2.00

Reverse

primerCACAGAACCGACCTGTGTCA Minus 20 1033 1014 59.90 55.00 7.00 3.00

Internal

oligo

Plus

Product

length70

Product Tm

Product Tm

-

min(OLIGO

Tm)

Exon

junction

Total intron

size

Products on intended target

Products on allowed transcript variants

Products on potentially unintended templates

Products on target templates

Primer pair 5

Sequence (5'->3') Template

strand LengthStart StopTm GC%

Self

complementarity

Self 3'

complementarity

er-Blast results http://www.ncbi.nlm.nih.gov/tools/primer-blast/prim

1/17/2014

8/13/2019 Primer NDV B1

4/4

Forward

primerACCGAAGGCGCACTTACTAC Plus 20 1169 1188 60.11 55.00 6.00 1.00

Reverse

primerCGAATTCCCCACTGAGCCTT Minus 20 1367 1348 60.04 55.00 6.00 1.00

Internal

oligoPlus

Product

length199

Product Tm

Product Tm

- min(OLIGO

Tm)

Exon

junction

Total intron

size

Products on intended target

Products on allowed transcript variants

Products on potentially unintended templates

Products on target templates

er-Blast results http://www.ncbi.nlm.nih.gov/tools/primer-blast/prim

1/17/2014