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
5956	5'	-59.6	NC_001806.1	+	109221	0.66	0.733827
	Target:  5'- gCUCC-CUUaGCGUggGGCCGgGCGGGGc- -3' miRNA:   3'- -GAGGcGAA-CGCA--CCGGCaCGCCUCaa -5'
5956	5'	-59.6	NC_001806.1	+	21754	0.66	0.733827
	Target:  5'- --aCGCgagGCGcgGGCCGUcggGCGGGGUc -3' miRNA:   3'- gagGCGaa-CGCa-CCGGCA---CGCCUCAa -5'
5956	5'	-59.6	NC_001806.1	+	120994	0.66	0.703473
	Target:  5'- aCUCCGUcuUUGUGUGGCgCGUcguucggGCGGAc-- -3' miRNA:   3'- -GAGGCG--AACGCACCG-GCA-------CGCCUcaa -5'
5956	5'	-59.6	NC_001806.1	+	23915	0.67	0.674562
	Target:  5'- -gCCGCUgccggGCGaggaccUGGCCGgcgGCGGGGc- -3' miRNA:   3'- gaGGCGAa----CGC------ACCGGCa--CGCCUCaa -5'
5956	5'	-59.6	NC_001806.1	+	4653	0.67	0.654444
	Target:  5'- uCUCCGCg-GCGgcugGGCCG-GCGGGc-- -3' miRNA:   3'- -GAGGCGaaCGCa---CCGGCaCGCCUcaa -5'
5956	5'	-59.6	NC_001806.1	+	126579	0.68	0.614065
	Target:  5'- gCUCCGCc-GCGgaucgGGCCuugGUGGAGUUa -3' miRNA:   3'- -GAGGCGaaCGCa----CCGGca-CGCCUCAA- -5'
5956	5'	-59.6	NC_001806.1	+	126110	0.69	0.554021
	Target:  5'- uUUCGCUacUGCGUgGGCCGcGCGGAc-- -3' miRNA:   3'- gAGGCGA--ACGCA-CCGGCaCGCCUcaa -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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