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
24944	5'	-56.2	NC_005284.1	+	10427	0.66	0.673879
	Target:  5'- aCGCGCagUCGGCAUAucggaauuuggcgacGCGGgcGG-CGCAa -3' miRNA:   3'- -GCGCGg-AGCCGUAU---------------UGUCa-CCaGCGU- -5'
24944	5'	-56.2	NC_005284.1	+	44393	0.68	0.546238
	Target:  5'- aGUGCCgcgGGCAUGGCAGUuucuucgacguagaGGuUCGCGc -3' miRNA:   3'- gCGCGGag-CCGUAUUGUCA--------------CC-AGCGU- -5'
24944	5'	-56.2	NC_005284.1	+	17489	0.69	0.4663
	Target:  5'- gGCGCCg-GGU----CGGUGGUCGCGu -3' miRNA:   3'- gCGCGGagCCGuauuGUCACCAGCGU- -5'
24944	5'	-56.2	NC_005284.1	+	11065	0.69	0.456352
	Target:  5'- uCGCGCUgaugaaUCaGCA-GAUGGUGGUCGCGa -3' miRNA:   3'- -GCGCGG------AGcCGUaUUGUCACCAGCGU- -5'
24944	5'	-56.2	NC_005284.1	+	21498	0.7	0.427217
	Target:  5'- cCGCGCugCUUGGCAUGGCGGccGG-CGCu -3' miRNA:   3'- -GCGCG--GAGCCGUAUUGUCa-CCaGCGu -5'
24944	5'	-56.2	NC_005284.1	+	8978	0.71	0.381208
	Target:  5'- uCGCGUCgagCGGUu--GCcGUGGUCGCGc -3' miRNA:   3'- -GCGCGGa--GCCGuauUGuCACCAGCGU- -5'
24944	5'	-56.2	NC_005284.1	+	31501	1.08	0.000856
	Target:  5'- gCGCGCCUCGGCAUAACAGUGGUCGCAu -3' miRNA:   3'- -GCGCGGAGCCGUAUUGUCACCAGCGU- -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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