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Find Arabidopsis protein homologs
Align Mimulus contig with Arabidopsis protein (ESTWISE)
Calculate intron positions/phases in Arabidopsis proteins
Find corresponding positions in Mimulus
unigenes
Design primers spanning introns in Mimulus unigenes (Primer3)
Mimulus unigenes
Arabidopsisgene models
Arabidopsis proteins
ESTs
Geneticallymap
Align Mimulus unigenesto Arabidopsis
proteins (ESTWISE)
Physically map
(hybridizeto BACs)
Design overgos within exons
Design SNP assayfrom sequenced alleles
At5g24550 27 FSTTPLNRYSFPPHFDFGVASSAYQYEGAVEEGGRSPSIWDNFTHAFPE + + P NR FPP F FG ASSAYQ+EGA EGG+ PSIWD +TH FPE YESKPFNRTDFPPGFLFGAASSAYQFEGAAFEGGKGPSIWDTYTHQFPE MgUnigene 90 tgtactacagtccgtctgggttgtctggggtgggagcaatgatacctcg aacactagcatccgtttgcccccaatagcctaggagcgtgacacaatca taggtccctttatttttattttttatattatatgaatttgttctcataa
At5g24550 173 IIDDFRNFARFCFQEFGDKVSMWTTFNEPYVYSVSGYDAG---NKAIGR I+DD+ +F +CF+ FGD+V W TFNEP+V++ GYD G A GR IVDDYLDFVELCFKNFGDRVKNWITFNEPFVFTNGGYDGGFLGTLAxGR CONTIG5 531 agggtcgtggcttaatggcgaataatagctgtaaggtgggtcgacgcgc ttaaatattatgtaatgagtaagtctaactttcaggaaggttgctcNgg tgcttgtcgatctgtcatttgtgcaccggcgcatgcctgaccgtacctg
At5g24550 219 CSKWVN CS W N CSSWxN MgUnigene 678 ttttNa gccgga cgggct