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
2624	5'	-53.6	NC_001491.2	+	64550	0.66	0.937012
	Target:  5'- --cGGCGUGGcccacGUCCAGCcaGUcGAGGGGg -3' miRNA:   3'- aauUCGUACC-----UAGGUCG--CAcCUCCUC- -5'
2624	5'	-53.6	NC_001491.2	+	25127	0.66	0.931863
	Target:  5'- --cGGCcgGGGgggccgccaacUCCAGCG-GcGAGGAGg -3' miRNA:   3'- aauUCGuaCCU-----------AGGUCGCaC-CUCCUC- -5'
2624	5'	-53.6	NC_001491.2	+	10952	0.67	0.920795
	Target:  5'- -aGAGCGguaggGGAggCCgAGCG-GGGGGAGc -3' miRNA:   3'- aaUUCGUa----CCUa-GG-UCGCaCCUCCUC- -5'
2624	5'	-53.6	NC_001491.2	+	95	0.67	0.920795
	Target:  5'- -gGGGCGUGGccggaAGCGgaaggGGAGGAGu -3' miRNA:   3'- aaUUCGUACCuagg-UCGCa----CCUCCUC- -5'
2624	5'	-53.6	NC_001491.2	+	11272	0.68	0.881508
	Target:  5'- aUAGGCAcuagagGGcgCCAGCGUacaGGGGAGu -3' miRNA:   3'- aAUUCGUa-----CCuaGGUCGCAc--CUCCUC- -5'
2624	5'	-53.6	NC_001491.2	+	1063	0.69	0.816137
	Target:  5'- -gGGGCG-GGGUUCAGCGUcagcGGAuGGAGg -3' miRNA:   3'- aaUUCGUaCCUAGGUCGCA----CCU-CCUC- -5'
2624	5'	-53.6	NC_001491.2	+	147509	1.07	0.004852
	Target:  5'- uUUAAGCAUGGAUCCAGCGUGGAGGAGg -3' miRNA:   3'- -AAUUCGUACCUAGGUCGCACCUCCUC- -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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