STITCHER 2.0

WELCOME TO STITCHER 2.0

Primers for overlapping PCR applications

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DETAILED OUTPUT GRAPHICS

STITCHER 2.0

LAUNCH STITCHER
DRAW YOUR OWN PRIMERS

STITCHER 2.0

LAUNCH STITCHER

STITCHER 2.0 Features

Fast, easy to use

Drop a sequence into the input field in FASTA format. You can view an exon intron map by entering exons in uppercase and introns in lowercase. Set the primer design parameters to whatever makes sense for your experiment (default guidelines are provided) and choose which output files you would like to see

Primer maps and output files

Visualize the location of all designed primers along the sequence by choosing the 'Primer sequence map'. Other output files provide comprehensive visual guides to the designed primers as well as the provided input sequence. Draw your own primers in specific locations by selecting the 'Primer drawing canvas'

Online Help

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Drop a sequence here in FASTA format:

>sample fastA format ATGACCAAGTTGAAAATCTACTTGTTCCTTGTTGTCTCGTTGACTACACTTGGGCAATACGCAGCTGAGCCGCAAAATGGAGAAATAATTCACGTATCTTCCCAACGTATACCCGGGCCTGAGCCGGCTTGTGCTCCGGCTAAGCCATGTTCCCCCGGAGTTATCgtaccagtttggcagccatcggaaaacctgtcagaatgcaaaatatggTTCCGTGCAATTGTCTATTTAATCGCATTGGCCTATTTATTCTTTGGTGTCTCAATTGTGGCGGATCGATTCATGGCGTCTATTGAAGTGATCACTTCTCAGCAGAAATCTGTGAAAATGAAGAAGATAACCGGTGAACATTTCACAATAATGGTACGTGTCTGGAATGAAACAGTCAGTAACCTGACGCTAATggctctcggatcctcagcccccgagattttgctctcggtcatTGAAATTTGCGGAAATAATTTCGAAGCTGGAGAGCTGGGACCATCGACAATTGTTGGATCAGCTGCTTTTAACCTATTCATTATTATTGCAGTCTGTATTATGGCTATTCCAAACGGCGAGACCCGTCGAGTACAACATAATGGTGTGTTCTGGGTtactgtagtttggtctacatttgCATACGTCTGGCTTTACCTAATCCTGAGTGTGTTCAGTCCGGGAGAAGTTGAAGTATGGGAGGGTGTGCTCACTTTTGTGTTTTTCCCGCTAACTGTgggcagtgcctactttgccgatgcacatgctgggcaattcggtcagagactaatctccggacccctctcctcgttcgtaaggaggtcaccaCGCCGTTCTCCGTCCAAAAAAACCCGGGAAAACGTGGAAAATGGAGCCGGACTCCCAGGGGATGCAACTCAAAATTTGATAGGAGGAGACGCcgacgccctggcatttgaaattcacagacgtcactaccTGGATATTTTCAAACAATTGAGATCGGAGCATCCAGATGCTCCAGTCGTTGAACTTGAGAAGCATGCCATGGAGAAAGTTGTCGGAGAGCAGAAGAAATCAAGAGCTTTTTATAGAATTcagacaactaggaaaatgatcggtagtggaGATATTCAGAAAAAATTGAAGAAAAGTAATAAACTGGAGCCAatggttgttcaaaaaaccatggccaccgtggagttcgaccctcctcactataCATGTCTGGAGAATGTTGGTGACGTGTACCTAACCGTCAAATGTGACCGAGGATCCGTACCAGAGGATACCA

Get Sequences

Retrieve sequences from NCBI in fastA format:
enter accession numbers as comma delimited list

Retrieve sequences from NCBI in ASN.1 format:

Primer Design Parameters

Get forward primers:
Yes No

Get reverse primers:
Yes No

Primer size:
Max: Min:

5' search area (bp):
start: end:

3' search area (bp):
distance from end: end number (default is sequence length):

Primer GC % forward primer:
Upper GC: Lower GC:

Primer GC % reverse primer:
Upper GC: Lower GC:

Primer Tm forward primer:
Upper Tm: Lower Tm:

Primer Tm reverse primer:
Upper Tm: Lower Tm:

Na⁺ concentration (mM):
10 50

K⁺ concentration (mM):
10 50

Increment forward:
Steps (bps):

Increment reverse:
Steps (bps):

GC clamp on forward primer:
Yes No

GC clamp on reverse primer:
Yes No

Remove N's:
Yes No

Maximum self-complementarity score:

Maximum 3' Self complementarity score:

Maximum overhang complementarity score:

Maximum primer dimer score:

Exclude repetitive sequence:
Yes No

Overlapping fragment:

User-defined overlap:

Mutant overlap (forward):

Output Files

Primer sequence map
Yes No

Input sequence features
Yes No

Primer Table
Yes No

Primer drawing canvas
Yes No

Primer features
Yes No