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
17499	5'	-52.1	NC_004456.1	+	33426	0.66	0.77266
	Target:  5'- uUGCCGGggcucagUCGaaGGCgAAGCAggagGCCAg -3' miRNA:   3'- -ACGGUCaa-----AGCa-CCGgUUUGUa---CGGU- -5'
17499	5'	-52.1	NC_004456.1	+	41284	0.67	0.737828
	Target:  5'- aUGCCAuacggcggGUGGCCAGGCGgacucGCCAg -3' miRNA:   3'- -ACGGUcaaag---CACCGGUUUGUa----CGGU- -5'
17499	5'	-52.1	NC_004456.1	+	30701	0.67	0.717673
	Target:  5'- cGCCAGUc---UGGUCAAAaAUGCCAu -3' miRNA:   3'- aCGGUCAaagcACCGGUUUgUACGGU- -5'
17499	5'	-52.1	NC_004456.1	+	16042	0.68	0.683437
	Target:  5'- aGCCGGguagcucggUCGUGGCCu----UGCCu -3' miRNA:   3'- aCGGUCaa-------AGCACCGGuuuguACGGu -5'
17499	5'	-52.1	NC_004456.1	+	21863	0.69	0.62545
	Target:  5'- aUGCgAa---CGUGGCCGAGuCAUGCCGc -3' miRNA:   3'- -ACGgUcaaaGCACCGGUUU-GUACGGU- -5'
17499	5'	-52.1	NC_004456.1	+	21158	0.69	0.590639
	Target:  5'- uUGCCaaAGgcacCGUGGUCGAugcuCAUGCCAu -3' miRNA:   3'- -ACGG--UCaaa-GCACCGGUUu---GUACGGU- -5'
17499	5'	-52.1	NC_004456.1	+	15317	0.71	0.478494
	Target:  5'- cUGaCCAGU---GUGGCCGGugAUGCCc -3' miRNA:   3'- -AC-GGUCAaagCACCGGUUugUACGGu -5'
17499	5'	-52.1	NC_004456.1	+	4217	1.09	0.001166
	Target:  5'- gUGCCAGUUUCGUGGCCAAACAUGCCAa -3' miRNA:   3'- -ACGGUCAAAGCACCGGUUUGUACGGU- -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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