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
26531	5'	-56.1	NC_005357.1	+	910	0.66	0.558816
	Target:  5'- uCAUCCCGGcCGcgGCAUugagugucagGGGGCCGa- -3' miRNA:   3'- cGUAGGGUCuGCa-UGUG----------CCCCGGUaa -5'
26531	5'	-56.1	NC_005357.1	+	4514	0.67	0.514198
	Target:  5'- gGCGgcgCCCGugaacguGGCGUGCugGGcGGUCGUg -3' miRNA:   3'- -CGUa--GGGU-------CUGCAUGugCC-CCGGUAa -5'
26531	5'	-56.1	NC_005357.1	+	24966	0.67	0.508852
	Target:  5'- uGCAggCCCuGGCGUggcACcuggccucgaugcugGCGGGGCCAc- -3' miRNA:   3'- -CGUa-GGGuCUGCA---UG---------------UGCCCCGGUaa -5'
26531	5'	-56.1	NC_005357.1	+	36337	0.68	0.432856
	Target:  5'- cCGUCCaaagcaCAGAuCGgguCGCGGGGCCGUa -3' miRNA:   3'- cGUAGG------GUCU-GCau-GUGCCCCGGUAa -5'
26531	5'	-56.1	NC_005357.1	+	538	0.69	0.376343
	Target:  5'- ---cCUCGGACGUGCGCG-GGCCGc- -3' miRNA:   3'- cguaGGGUCUGCAUGUGCcCCGGUaa -5'
26531	5'	-56.1	NC_005357.1	+	10065	0.71	0.286371
	Target:  5'- aGCGUCCgAGGCGU-CGuCGGGGCgAg- -3' miRNA:   3'- -CGUAGGgUCUGCAuGU-GCCCCGgUaa -5'
26531	5'	-56.1	NC_005357.1	+	5939	1.08	0.000683
	Target:  5'- gGCAUCCCAGACGUACACGGGGCCAUUg -3' miRNA:   3'- -CGUAGGGUCUGCAUGUGCCCCGGUAA- -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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