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
22028	3'	-50.6	NC_004927.1	+	73966	0.66	0.947633
	Target:  5'- --aCCGcGAGcGCGACGGAacagcucgccgcAGUUGCgGCg -3' miRNA:   3'- gaaGGU-CUC-CGUUGCCU------------UCAACGaUG- -5'
22028	3'	-50.6	NC_004927.1	+	31911	0.66	0.947633
	Target:  5'- --cCCugAGGGGCGAuuCGGggGcUGUUACa -3' miRNA:   3'- gaaGG--UCUCCGUU--GCCuuCaACGAUG- -5'
22028	3'	-50.6	NC_004927.1	+	75547	0.66	0.937615
	Target:  5'- uUUCCAGucgGGGUcggAugGGGAGgggucgGCUACu -3' miRNA:   3'- gAAGGUC---UCCG---UugCCUUCaa----CGAUG- -5'
22028	3'	-50.6	NC_004927.1	+	26564	0.67	0.932175
	Target:  5'- -gUCCGGGGugguaGCGGCGGAGGUggGUcgGCa -3' miRNA:   3'- gaAGGUCUC-----CGUUGCCUUCAa-CGa-UG- -5'
22028	3'	-50.6	NC_004927.1	+	53965	0.68	0.900654
	Target:  5'- gUUCCAGcGGgGACGGAGGUU-CaACa -3' miRNA:   3'- gAAGGUCuCCgUUGCCUUCAAcGaUG- -5'
22028	3'	-50.6	NC_004927.1	+	50334	0.68	0.886061
	Target:  5'- -aUCCgcuGGAGGCGGCGGAgcaGGUgGCa-- -3' miRNA:   3'- gaAGG---UCUCCGUUGCCU---UCAaCGaug -5'
22028	3'	-50.6	NC_004927.1	+	7778	1.11	0.002753
	Target:  5'- gCUUCCAGAGGCAACGGAAGUUGCUACa -3' miRNA:   3'- -GAAGGUCUCCGUUGCCUUCAACGAUG- -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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