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
17991	3'	-56	NC_004665.1	+	35664	0.66	0.566433
	Target:  5'- -aGUUCCCGCUCAcGCaGGUCCuuGuCAu -3' miRNA:   3'- cgCAAGGGUGAGU-UG-CUAGGggCcGU- -5'
17991	3'	-56	NC_004665.1	+	18127	0.66	0.544492
	Target:  5'- cGCcaUCUCGCUugguccagcgcaCAGCGAUCCaCGGCAg -3' miRNA:   3'- -CGcaAGGGUGA------------GUUGCUAGGgGCCGU- -5'
17991	3'	-56	NC_004665.1	+	4018	0.66	0.544492
	Target:  5'- gGCGUugucgUCCCACcagUCGAuggUGAUCCauaCGGCGc -3' miRNA:   3'- -CGCA-----AGGGUG---AGUU---GCUAGGg--GCCGU- -5'
17991	3'	-56	NC_004665.1	+	3705	0.67	0.490999
	Target:  5'- aGCGUgCCCAuCUCAGgGAUCggUGGCAu -3' miRNA:   3'- -CGCAaGGGU-GAGUUgCUAGggGCCGU- -5'
17991	3'	-56	NC_004665.1	+	21245	0.67	0.490999
	Target:  5'- aGCGUUCgCCACgUCAGCGuuaggGUCCCCcuCAa -3' miRNA:   3'- -CGCAAG-GGUG-AGUUGC-----UAGGGGccGU- -5'
17991	3'	-56	NC_004665.1	+	2937	0.69	0.410997
	Target:  5'- uUGUUCCaaggacacgaCGCUCggUGAucUCCCCGGUg -3' miRNA:   3'- cGCAAGG----------GUGAGuuGCU--AGGGGCCGu -5'
17991	3'	-56	NC_004665.1	+	33806	1.1	0.000467
	Target:  5'- gGCGUUCCCACUCAACGAUCCCCGGCAu -3' miRNA:   3'- -CGCAAGGGUGAGUUGCUAGGGGCCGU- -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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