RJPrimers
Transposable elements based PCR pimer design
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Choose primer type:

Identify repetitive DNA junctions and then design RJM primer pairs. One primer of a RJM primer pair includes the TE junction, and another primer can be picked from another TE or gene sequence.

Reset the entire form

Repeat Databases: (one or more databases can be chosen)

RepBase14.07 MIPS REdat v4.3 TREP complete Maize TEDB
TIGR Triticum Repeats v3.0 TIGR Brassicaceae Repeats v2.0 TIGR Fabaceae Repeats v2.0 TIGR Gramineae Repeats v2.0
TIGR Solanaceae Repeats v3.2 TIGR Arabidopsis_Repeats TIGR Brassica Repeats v2.0 TIGR Glycine Repeats v2.0
TIGR Hordeum Repeats v3.0 TIGR Oryza Repeats v3.3 TIGR Sorghum Repeats v3.0 TIGR Solanum Repeats v3.2
TIGR Medicago Repeats v2.0

Input Sequences: (the maximum of 200 short sequences (< 1.5kb) at a time will be processed)

Upload sequence file in FASTA format:     
OR copy/paste source sequences in FASTA format.        Example sequences      Clear sequence only

Parameters for repetitive DNA junction identification

Minimum E-value for all hits Minimum E-value for the top hit

General Settings for Primers

Product Size Min: Opt: (0 for no Opt) Max:
Max 3' Stability:
Primer Size Min: Opt: Max:
Primer Tm Min: Opt: Max: Max Tm Difference:
Product Tm Min: Opt: Max:
Primer GC% Min: Opt: Max:
Max Self Complementarity: Max 3' Self Complementarity:      
Max #N's: Max Poly-X: CG Clamp:  
Salt Concentration: Annealing Oligo Concentration: (Not the concentration of oligos in the reaction mix but of those annealing to template.)