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
21934	3'	-49.6	NC_004913.1	+	37082	0.66	0.967952
	Target:  5'- aGGGAgcuACAGGCUccuuuuuuauUAUucgCAUUCACCCu -3' miRNA:   3'- -CCUUau-UGUCCGA----------AUG---GUAGGUGGGc -5'
21934	3'	-49.6	NC_004913.1	+	17172	0.66	0.960621
	Target:  5'- cGggUGGgAGGcCUUGCCAcuUCCAgucUCCGu -3' miRNA:   3'- cCuuAUUgUCC-GAAUGGU--AGGU---GGGC- -5'
21934	3'	-49.6	NC_004913.1	+	3569	0.68	0.907018
	Target:  5'- uGAGUAAauaAGGCUUAUCG-CUGCCCc -3' miRNA:   3'- cCUUAUUg--UCCGAAUGGUaGGUGGGc -5'
21934	3'	-49.6	NC_004913.1	+	53466	0.69	0.875075
	Target:  5'- cGGAAUGaugucguuauauuuACAGGCga--CA-CCGCCCGg -3' miRNA:   3'- -CCUUAU--------------UGUCCGaaugGUaGGUGGGC- -5'
21934	3'	-49.6	NC_004913.1	+	16402	0.69	0.869395
	Target:  5'- aGggUGGCAGGaUUACaaaaauauccUCCGCCCGg -3' miRNA:   3'- cCuuAUUGUCCgAAUGgu--------AGGUGGGC- -5'
21934	3'	-49.6	NC_004913.1	+	3876	0.71	0.754723
	Target:  5'- gGGAAUGACGuGUUUACCGUCgcgggugagCACCCc -3' miRNA:   3'- -CCUUAUUGUcCGAAUGGUAG---------GUGGGc -5'
21934	3'	-49.6	NC_004913.1	+	56100	1.13	0.002282
	Target:  5'- aGGAAUAACAGGCUUACCAUCCACCCGg -3' miRNA:   3'- -CCUUAUUGUCCGAAUGGUAGGUGGGC- -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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