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
27930	5'	-50.8	NC_005886.2	+	26109	0.66	0.909797
	Target:  5'- uUCCCG-CG-UCAC-CUUCCGAuACAGg -3' miRNA:   3'- -GGGGCuGCuAGUGaGAAGGCU-UGUUg -5'
27930	5'	-50.8	NC_005886.2	+	42791	0.66	0.90297
	Target:  5'- aCUCGAUGuuUCAUUCgagCCGAuCAACa -3' miRNA:   3'- gGGGCUGCu-AGUGAGaa-GGCUuGUUG- -5'
27930	5'	-50.8	NC_005886.2	+	10770	0.68	0.838515
	Target:  5'- uCCCCGGCGcaGUCACUCcaUUCaCGcuCAAg -3' miRNA:   3'- -GGGGCUGC--UAGUGAG--AAG-GCuuGUUg -5'
27930	5'	-50.8	NC_005886.2	+	5416	0.68	0.828404
	Target:  5'- aCCUgcgcaagUGGCGAUCAUgg-UUCGAGCAACg -3' miRNA:   3'- -GGG-------GCUGCUAGUGagaAGGCUUGUUG- -5'
27930	5'	-50.8	NC_005886.2	+	31821	0.69	0.759536
	Target:  5'- aUCCCGuACGGUCACgg-UgCGAAUGGCa -3' miRNA:   3'- -GGGGC-UGCUAGUGagaAgGCUUGUUG- -5'
27930	5'	-50.8	NC_005886.2	+	191	0.74	0.525958
	Target:  5'- gCCCGGCaaagGAUCGCUCgcUgGAACAACg -3' miRNA:   3'- gGGGCUG----CUAGUGAGaaGgCUUGUUG- -5'
27930	5'	-50.8	NC_005886.2	+	15116	0.83	0.161005
	Target:  5'- uCCCCGcGCGAUCAUUCaUCCGAcCGACg -3' miRNA:   3'- -GGGGC-UGCUAGUGAGaAGGCUuGUUG- -5'
27930	5'	-50.8	NC_005886.2	+	17693	1.13	0.001529
	Target:  5'- gCCCCGACGAUCACUCUUCCGAACAACa -3' miRNA:   3'- -GGGGCUGCUAGUGAGAAGGCUUGUUG- -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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