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
1305	5'	-53.3	NC_001331.1	+	3847	0.66	0.267831
	Target:  5'- gAUCCGCCGAUcggcgaagggauGGGcguUCAGAUcaacaGGCGCa -3' miRNA:   3'- gUAGGUGGCUG------------UCC---AGUUUG-----UCGCGg -5'
1305	5'	-53.3	NC_001331.1	+	4259	0.66	0.2521
	Target:  5'- --gCCGCCauGAgGGG-CGGGCcGCGCCg -3' miRNA:   3'- guaGGUGG--CUgUCCaGUUUGuCGCGG- -5'
1305	5'	-53.3	NC_001331.1	+	292	0.68	0.18459
	Target:  5'- gAUCUGCUGGCcguGGgcggCAAGCcgauGGCGCCg -3' miRNA:   3'- gUAGGUGGCUGu--CCa---GUUUG----UCGCGG- -5'
1305	5'	-53.3	NC_001331.1	+	3472	0.68	0.178796
	Target:  5'- --gCCAUCGGCGGG-CGGACgguugaguugGGCGUCa -3' miRNA:   3'- guaGGUGGCUGUCCaGUUUG----------UCGCGG- -5'
1305	5'	-53.3	NC_001331.1	+	1991	0.69	0.138005
	Target:  5'- gAUCCACCGACccgaccacgccGGG-CGguGACGGCGgCg -3' miRNA:   3'- gUAGGUGGCUG-----------UCCaGU--UUGUCGCgG- -5'
1305	5'	-53.3	NC_001331.1	+	4500	0.69	0.138005
	Target:  5'- aGUUCACCGACuuGUCAGGC-GUGCg -3' miRNA:   3'- gUAGGUGGCUGucCAGUUUGuCGCGg -5'
1305	5'	-53.3	NC_001331.1	+	4623	1.13	4e-05
	Target:  5'- aCAUCCACCGACAGGUCAAACAGCGCCa -3' miRNA:   3'- -GUAGGUGGCUGUCCAGUUUGUCGCGG- -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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