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
11333	5'	-56.1	NC_003084.1	+	81292	0.66	0.835585
	Target:  5'- cGUCCcaaaaGGGUaaaCGguUGCccagcuuggcgAUACCCUCGAu -3' miRNA:   3'- -CAGG-----UCCAg--GCguACG-----------UAUGGGAGCU- -5'
11333	5'	-56.1	NC_003084.1	+	52354	0.66	0.827011
	Target:  5'- -aCgAGGUCCGCGUGauggauucCAaGCUCUCGGc -3' miRNA:   3'- caGgUCCAGGCGUAC--------GUaUGGGAGCU- -5'
11333	5'	-56.1	NC_003084.1	+	92364	0.67	0.789992
	Target:  5'- -aCCAGGUCaCGCAcaacucgUGCAcuuuUACCCUUc- -3' miRNA:   3'- caGGUCCAG-GCGU-------ACGU----AUGGGAGcu -5'
11333	5'	-56.1	NC_003084.1	+	95434	0.67	0.781507
	Target:  5'- -cCCaugGGGUCCGCGaGCGUACUgUUGGc -3' miRNA:   3'- caGG---UCCAGGCGUaCGUAUGGgAGCU- -5'
11333	5'	-56.1	NC_003084.1	+	92176	0.67	0.771945
	Target:  5'- uGUCCAGGUUgaugauuauUGUacGUGCGUACCagCUCGGu -3' miRNA:   3'- -CAGGUCCAG---------GCG--UACGUAUGG--GAGCU- -5'
11333	5'	-56.1	NC_003084.1	+	760	0.69	0.660264
	Target:  5'- uGUUCAGGUCgCGC-UGCAcAUCUUCGGc -3' miRNA:   3'- -CAGGUCCAG-GCGuACGUaUGGGAGCU- -5'
11333	5'	-56.1	NC_003084.1	+	47348	1.09	0.001744
	Target:  5'- cGUCCAGGUCCGCAUGCAUACCCUCGAa -3' miRNA:   3'- -CAGGUCCAGGCGUACGUAUGGGAGCU- -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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