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
17636	5'	-51.9	NC_004466.2	+	12886	0.66	0.808605
	Target:  5'- -aAUUCCCCaAGGUGCuaucuUCGGGGGu-- -3' miRNA:   3'- uaUAAGGGG-UCUAUGu----GGCCUCCuau -5'
17636	5'	-51.9	NC_004466.2	+	11217	0.67	0.767061
	Target:  5'- ----gCCCCAGAUGguCUGGuGGAg- -3' miRNA:   3'- uauaaGGGGUCUAUguGGCCuCCUau -5'
17636	5'	-51.9	NC_004466.2	+	36780	0.67	0.765987
	Target:  5'- gGUGUUCCCCAugugauguacgucGAggGCACC-GAGGAa- -3' miRNA:   3'- -UAUAAGGGGU-------------CUa-UGUGGcCUCCUau -5'
17636	5'	-51.9	NC_004466.2	+	5180	0.68	0.711749
	Target:  5'- ---aUCCCCAGAguUAUACUGGAGu--- -3' miRNA:   3'- uauaAGGGGUCU--AUGUGGCCUCcuau -5'
17636	5'	-51.9	NC_004466.2	+	31295	0.69	0.630993
	Target:  5'- ----aCCUCAGcgACuucCCGGAGGAUAu -3' miRNA:   3'- uauaaGGGGUCuaUGu--GGCCUCCUAU- -5'
17636	5'	-51.9	NC_004466.2	+	5965	0.72	0.431229
	Target:  5'- -cAUUUCCCAGAUACGCaucaGGuGGAg- -3' miRNA:   3'- uaUAAGGGGUCUAUGUGg---CCuCCUau -5'
17636	5'	-51.9	NC_004466.2	+	2490	0.73	0.40143
	Target:  5'- ---cUCCCUgGGAUACuggACCGGAGGAUAc -3' miRNA:   3'- uauaAGGGG-UCUAUG---UGGCCUCCUAU- -5'
17636	5'	-51.9	NC_004466.2	+	1049	1.05	0.002449
	Target:  5'- gAUAUUCCCCAGAUACACCGGAGGAUAa -3' miRNA:   3'- -UAUAAGGGGUCUAUGUGGCCUCCUAU- -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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