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
22824	5'	-55.4	NC_005135.1	+	121425	0.66	0.953969
	Target:  5'- aCGAUCGaAGaUCGcCAGUCuGUCGGCCGg -3' miRNA:   3'- cGCUGGCaUC-AGU-GUUAG-CGGCCGGU- -5'
22824	5'	-55.4	NC_005135.1	+	77159	0.66	0.953969
	Target:  5'- gGCGGCCGacauucuuuuucgGGUUuaaccucgaauaaaaACAcGUCGCCGGUCAc -3' miRNA:   3'- -CGCUGGCa------------UCAG---------------UGU-UAGCGGCCGGU- -5'
22824	5'	-55.4	NC_005135.1	+	147293	0.66	0.949959
	Target:  5'- -aGGCCGUGGUUuguuucagaaGCA--CGCCGGgCAg -3' miRNA:   3'- cgCUGGCAUCAG----------UGUuaGCGGCCgGU- -5'
22824	5'	-55.4	NC_005135.1	+	58966	0.66	0.931126
	Target:  5'- uGCGACCGUgaAGUCcgcgagcaauaugACAAUUGCUuaGGCa- -3' miRNA:   3'- -CGCUGGCA--UCAG-------------UGUUAGCGG--CCGgu -5'
22824	5'	-55.4	NC_005135.1	+	88369	0.68	0.876864
	Target:  5'- cGCGAuaCCGUccauauauGUCACGAaugugaugguaUCGCCGGCa- -3' miRNA:   3'- -CGCU--GGCAu-------CAGUGUU-----------AGCGGCCGgu -5'
22824	5'	-55.4	NC_005135.1	+	104561	0.68	0.859991
	Target:  5'- gGCGACCacGGUUACGAUCcuaccaacaucgcuGCUGGUCAa -3' miRNA:   3'- -CGCUGGcaUCAGUGUUAG--------------CGGCCGGU- -5'
22824	5'	-55.4	NC_005135.1	+	90189	1.11	0.003257
	Target:  5'- gGCGACCGUAGUCACAAUCGCCGGCCAg -3' miRNA:   3'- -CGCUGGCAUCAGUGUUAGCGGCCGGU- -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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