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
32837	5'	-48.2	NC_007346.1	+	71346	0.66	0.999992
	Target:  5'- cACCA---ACGCUUUCGGaaaACAGaCAAg -3' miRNA:   3'- uUGGUaaaUGUGAAAGCCg--UGUC-GUU- -5'
32837	5'	-48.2	NC_007346.1	+	78001	0.66	0.999978
	Target:  5'- uGGCCAcgUAugcCGCUUgCGGUACAGCGu -3' miRNA:   3'- -UUGGUaaAU---GUGAAaGCCGUGUCGUu -5'
32837	5'	-48.2	NC_007346.1	+	80525	0.67	0.999931
	Target:  5'- -uCCAUUUAUACaacUCGGCAUAuGCAc -3' miRNA:   3'- uuGGUAAAUGUGaa-AGCCGUGU-CGUu -5'
32837	5'	-48.2	NC_007346.1	+	138165	0.67	0.99991
	Target:  5'- gGACCGgggcGCACgagCGGCGgAGCGAg -3' miRNA:   3'- -UUGGUaaa-UGUGaaaGCCGUgUCGUU- -5'
32837	5'	-48.2	NC_007346.1	+	216275	0.68	0.999807
	Target:  5'- --aCAUUUACAU--UUGGUACAGCGGa -3' miRNA:   3'- uugGUAAAUGUGaaAGCCGUGUCGUU- -5'
32837	5'	-48.2	NC_007346.1	+	280466	0.68	0.99969
	Target:  5'- gGugCAgUUGCACccgUUUCGcGCGCGGCAGg -3' miRNA:   3'- -UugGUaAAUGUG---AAAGC-CGUGUCGUU- -5'
32837	5'	-48.2	NC_007346.1	+	147044	0.73	0.984927
	Target:  5'- uGCCAUggACGCUauaaUUUGGUGCGGCAAu -3' miRNA:   3'- uUGGUAaaUGUGA----AAGCCGUGUCGUU- -5'
32837	5'	-48.2	NC_007346.1	+	322589	1.04	0.058303
	Target:  5'- gAACCAUUUACACUUUCGGCACAGCAAc -3' miRNA:   3'- -UUGGUAAAUGUGAAAGCCGUGUCGUU- -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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