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
27922	3'	-51.7	NC_005886.2	+	4306	0.68	0.757972
	Target:  5'- -aCGGUGACACGCUCacugGCGuGGu -3' miRNA:   3'- ugGCCAUUGUGCGAGcauaCGUuCCu -5'
27922	3'	-51.7	NC_005886.2	+	34560	0.68	0.757972
	Target:  5'- gGCUGGUugcuuauuCACGCUgCGcGUGCGGGGu -3' miRNA:   3'- -UGGCCAuu------GUGCGA-GCaUACGUUCCu -5'
27922	3'	-51.7	NC_005886.2	+	41879	0.68	0.751542
	Target:  5'- uACCGGccGGCGCGUUCGgguugaucgccugcgUAUGCAuguGGAc -3' miRNA:   3'- -UGGCCa-UUGUGCGAGC---------------AUACGUu--CCU- -5'
27922	3'	-51.7	NC_005886.2	+	15594	0.69	0.714298
	Target:  5'- -aCGGUAAUACGCUCGaucuUGCGcuGAu -3' miRNA:   3'- ugGCCAUUGUGCGAGCau--ACGUucCU- -5'
27922	3'	-51.7	NC_005886.2	+	40954	0.71	0.577982
	Target:  5'- -aCGGUAACAgcagaagcuauCGCaUCGgagGUGCAAGGGg -3' miRNA:   3'- ugGCCAUUGU-----------GCG-AGCa--UACGUUCCU- -5'
27922	3'	-51.7	NC_005886.2	+	7145	0.75	0.352953
	Target:  5'- uGCCGGUGcuCGCGCUCGgugGCGGcGGAu -3' miRNA:   3'- -UGGCCAUu-GUGCGAGCauaCGUU-CCU- -5'
27922	3'	-51.7	NC_005886.2	+	7679	1.09	0.001829
	Target:  5'- gACCGGUAACACGCUCGUAUGCAAGGAu -3' miRNA:   3'- -UGGCCAUUGUGCGAGCAUACGUUCCU- -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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