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
14715	5'	-56	NC_003529.1	+	10330	0.66	0.889595
	Target:  5'- -gUGCCUCUGguUga-GGCGCGAAGCu -3' miRNA:   3'- aaGCGGAGGCguGuacCCGUGCUUUG- -5'
14715	5'	-56	NC_003529.1	+	47766	0.66	0.860304
	Target:  5'- -cCGCCUguugcauuaUUGCACAUGGcaaaccGCugGAAACg -3' miRNA:   3'- aaGCGGA---------GGCGUGUACC------CGugCUUUG- -5'
14715	5'	-56	NC_003529.1	+	67917	0.67	0.836091
	Target:  5'- -gCGCCUugUCGaCACGuUGGcGCACGAAAUg -3' miRNA:   3'- aaGCGGA--GGC-GUGU-ACC-CGUGCUUUG- -5'
14715	5'	-56	NC_003529.1	+	98737	0.68	0.772354
	Target:  5'- cUCGUCUCCGUACAUuucaaacGGGguCGucAAACa -3' miRNA:   3'- aAGCGGAGGCGUGUA-------CCCguGC--UUUG- -5'
14715	5'	-56	NC_003529.1	+	89223	0.7	0.701125
	Target:  5'- --aGCCUCCGgACAcaaUGGGCGCaucgaaaaaacgcuGAAACu -3' miRNA:   3'- aagCGGAGGCgUGU---ACCCGUG--------------CUUUG- -5'
14715	5'	-56	NC_003529.1	+	126511	0.75	0.381071
	Target:  5'- -gCGUgUCUGCACAUGGGaCACGAAu- -3' miRNA:   3'- aaGCGgAGGCGUGUACCC-GUGCUUug -5'
14715	5'	-56	NC_003529.1	+	21161	1.06	0.003833
	Target:  5'- cUUCGCCUCCGCACAUGGGCACGAAACc -3' miRNA:   3'- -AAGCGGAGGCGUGUACCCGUGCUUUG- -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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