miRNA display CGI

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ID	Location	Perfect MFE.*	RefSeq Acc.	strand	Start Position	R_P_ratio#	P value
	Predicted miRNA align pattern
375	3'	-55.2	AC_000011.1	+	25502	0.66	0.599104
	Target:  5'- gUCUGGGGGUCGaGGUAGAcCCCGc- -3' miRNA:   3'- aGGGUCCCCGGCaUCAUUUaGGGUcu -5'
375	3'	-55.2	AC_000011.1	+	9433	0.66	0.587786
	Target:  5'- cUCCAGGuGGCCG-GGggGGUCCCc-- -3' miRNA:   3'- aGGGUCC-CCGGCaUCauUUAGGGucu -5'
375	3'	-55.2	AC_000011.1	+	4132	0.67	0.521023
	Target:  5'- gCUCGGGGGUgGUGuuGUAAAUcaCCCAGu -3' miRNA:   3'- aGGGUCCCCGgCAU--CAUUUA--GGGUCu -5'
375	3'	-55.2	AC_000011.1	+	18012	0.67	0.521023
	Target:  5'- -gCCAGGGGCgcgaugggccgCGUGGUGGGcagaCCCAGu -3' miRNA:   3'- agGGUCCCCG-----------GCAUCAUUUa---GGGUCu -5'
375	3'	-55.2	AC_000011.1	+	4094	0.69	0.43715
	Target:  5'- gUCCCGGGGGUgGaGGUAGcUCCauugCAGGg -3' miRNA:   3'- -AGGGUCCCCGgCaUCAUUuAGG----GUCU- -5'
375	3'	-55.2	AC_000011.1	+	18716	0.71	0.303292
	Target:  5'- cUCCCuuGGGGGCCagacuguuGUAGgcGGUgCCGGAg -3' miRNA:   3'- -AGGG--UCCCCGG--------CAUCauUUAgGGUCU- -5'
375	3'	-55.2	AC_000011.1	+	4635	0.72	0.266263
	Target:  5'- aUCCCGGGGG-CGUAGUuccccucacAGAucugcaucUCCCAGGc -3' miRNA:   3'- -AGGGUCCCCgGCAUCA---------UUU--------AGGGUCU- -5'
375	3'	-55.2	AC_000011.1	+	27907	1.09	0.000529
	Target:  5'- cUCCCAGGGGCCGUAGUAAAUCCCAGAg -3' miRNA:   3'- -AGGGUCCCCGGCAUCAUUUAGGGUCU- -5'

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Note:
      When operating RNAhybrid, the pipeline first calculates the perfect minimum free energy (Perfect mfe *) of a putative miRNA when the entire putative miRNA binds to a perfectly complementary target site, then it calculates the minimum free energy of RNA duplex (mfe of the miRNA/mRNA duplex), abbreviated as Rd_mfe. An alignment for which the Rd_mfe to its correspondent Perfect mfe ratio (R_P_ratio #) is more than 66% is regarded as a positive alignment as described by Krek et al. (21). The P_value is calculated by RNAhybrid.

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