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
2330	3'	-58	NC_001416.1	+	10864	0.66	0.509024
	Target:  5'- gUUGCaGCAggaUCAGCCAcGGAcuuUGCCCGc -3' miRNA:   3'- aGACGcCGUa--GGUCGGU-CCU---AUGGGC- -5'
2330	3'	-58	NC_001416.1	+	9170	0.67	0.476189
	Target:  5'- aUCUGcCGGagauaCCAGCUucacgcuggcguGGAUGCCCGg -3' miRNA:   3'- -AGAC-GCCgua--GGUCGGu-----------CCUAUGGGC- -5'
2330	3'	-58	NC_001416.1	+	4547	0.67	0.462156
	Target:  5'- -aUGCGGUGUCCGGCgacagccugacugccCAGGAggcACUCGc -3' miRNA:   3'- agACGCCGUAGGUCG---------------GUCCUa--UGGGC- -5'
2330	3'	-58	NC_001416.1	+	740	0.68	0.391886
	Target:  5'- gCUGCGGCAuuuugUCCGcGCCGGGcuucGCUCa -3' miRNA:   3'- aGACGCCGU-----AGGU-CGGUCCua--UGGGc -5'
2330	3'	-58	NC_001416.1	+	394	0.69	0.356911
	Target:  5'- aCUGCGGCAggCCAGCgAGGcagAUCUc -3' miRNA:   3'- aGACGCCGUa-GGUCGgUCCua-UGGGc -5'
2330	3'	-58	NC_001416.1	+	843	0.72	0.233507
	Target:  5'- gUCUGUGGC-UCCGGCCugaacagugAGcGAaGCCCGg -3' miRNA:   3'- -AGACGCCGuAGGUCGG---------UC-CUaUGGGC- -5'
2330	3'	-58	NC_001416.1	+	3533	1.08	0.000464
	Target:  5'- uUCUGCGGCAUCCAGCCAGGAUACCCGu -3' miRNA:   3'- -AGACGCCGUAGGUCGGUCCUAUGGGC- -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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