* entries are required

1. *Please copy & paste in the primer(s) data in proper format:

or upload data file

2. Please select the chromosome the primers are mapping to:

   * Chromosome 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y of latest version of UCSC freeze (be sure to select the correct one)

3. Adjustable parameters.

Additional parameters for BLAST to set:

• E value   (the lower the value, the more stringent the cutoff. NCBI default 10.  If analyzing short fragments like oligos, use 10 or higher.)

For annotation,

•  First filter

@ Minimum size of match for valid hits  bp (If your primer is shorter, please decrease this number accordingly)

@ Minimum percentage of identities for valid hits 95% 96% 97% 98% 99% 100%

@ The maximum length difference between query primer and matching fragment is bp

•  Second filter

        @ Only the best matches will be used for annotation All hits above filter will be used for annotation

4. Choice of outputs:

    Show BLAST annotation evidence of match identity percentage in Genbank annotation and features table

    Annotation Genbank format data or Genbank format features (gbheader)

         viewable in Vector NTI  or Artemis

    Feature table ready for database in tab-delimited format 

    Features failed to be annotated

    Duplicated features (possibly false positive due to homologs)

    Original BLAST output

    Data for the "customTrack" of Genome Browser
         Name the track as
    Annotation evidence (compact parsed BLAST data)

    Original full-length Genbank format data (with sequence body)

    Original gbheader

5. Please specify the email address to which the outputs will be delivered:

 Email address *

choice of output in gzip compressed format: yes, zip it no, original data please

Your email box accepts message size limit of  1 MB 2 MB 4 MB 6 MB per message

If your input data file is from a Mac machine, please be sure to check this box