Sequences should be in the one-letter-code ({a,b,c,g,h,k,m,n,r,s,t,u,w,y}), upper or lower case; all other characters are ignored during input. Multiple sequence input is accepted in FASTA format (sequences separated by identifier lines of the form “>SQ;name_of_sequence comments”) or in GenBank format.

Paste your genomic DNA sequence here:

... or upload your sequence file (specify file name):

... or type in the GenBank accession number of your sequence:

Select format: plain FASTA GenBank
Sequence name: (optional, used in plain sequence format only)
From position: to position: Strand: original reverse both

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Parameters:

Species human mouse rat chicken Drosophila nematode yeast Aspergillus Arabidopsis maize rice Medicago generic Cutoff 12.0 9.0 6.0 3.0 0.0 -99.9 Local pruning on off Score non-canonical sites on off

Order sites by position P-value *-value
P-value threshold: 0.9 0.75 0.50 0.25 0 not set (overrides Cutoff option)
*-value threshold: 14 (highly likely sites) 11 (likely sites) 8 (possible sites) 5 (uncertain sites) 3 (all sites) not set (restricts Cutoff and P-value threshold options)
Display highest scoring sites only. Set to: 4 highest scoring sites 10 highest scoring sites 20 highest scoring sites 50 highest scoring sites 100 highest scoring sites all sites not set (you must select ordering by P-value or *-value above)

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Spliced Alignment:

The output will show an optimal threading of a cDNA/EST or protein sequence into the genomic DNA by aligning putative exons only and displaying putative introns as (long) gaps in the cDNA/EST or protein target.

Current limitations when using this option: genomic DNA <= 15,000 nucleotides, cDNA/EST <= 8,000 nucleotides, protein targets <= 3,000 amino acids.

Paste your cDNA/EST sequence(s) here ( FASTA format ):

... and/or upload your cDNA/EST sequence file (specify file name):

Strand to align: + strand only both + and - strand

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Paste your target protein sequence(s) here:

... and/or upload your target protein sequence file (specify file name):

Submit job:

Select "Submit" to send the job to the server. By default, output will be posted to your browser. You may select to have the ouput sent to you by email instead. Selection of this option is advised in the rare case that output posting is slow due to server overload.

Click here to send the output to this email address:

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