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
23108	3'	-49.1	NC_005178.1	+	10773	0.65	0.922929
	Target:  5'- --cUGCCCCUUGGUCAguugcuccaggcguUCcucGGGUGUc -3' miRNA:   3'- guaAUGGGGGACUAGU--------------AGua-CCUACG- -5'
23108	3'	-49.1	NC_005178.1	+	4958	0.66	0.897158
	Target:  5'- ---cGCCCgCUGAUCAUCGacgaaaUGGAc-- -3' miRNA:   3'- guaaUGGGgGACUAGUAGU------ACCUacg -5'
23108	3'	-49.1	NC_005178.1	+	708	0.66	0.921002
	Target:  5'- gCGUUGauCCCCUUGAuauaUCuguaaagcugggucUCGUGGAUGCc -3' miRNA:   3'- -GUAAU--GGGGGACU----AGu-------------AGUACCUACG- -5'
23108	3'	-49.1	NC_005178.1	+	6316	0.67	0.864544
	Target:  5'- --gUGCCUCCUuGUCAgUCGUGGGaccgccUGCg -3' miRNA:   3'- guaAUGGGGGAcUAGU-AGUACCU------ACG- -5'
23108	3'	-49.1	NC_005178.1	+	12269	0.68	0.837103
	Target:  5'- ---cACCCUgCUGAagGUCAgcgcGGAUGCg -3' miRNA:   3'- guaaUGGGG-GACUagUAGUa---CCUACG- -5'
23108	3'	-49.1	NC_005178.1	+	33445	0.72	0.602057
	Target:  5'- ---cACCCUgCUGG-CGUCGUGGAUGUc -3' miRNA:   3'- guaaUGGGG-GACUaGUAGUACCUACG- -5'
23108	3'	-49.1	NC_005178.1	+	14120	1.12	0.001703
	Target:  5'- gCAUUACCCCCUGAUCAUCAUGGAUGCc -3' miRNA:   3'- -GUAAUGGGGGACUAGUAGUACCUACG- -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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