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
22159	5'	-49.9	NC_004927.1	+	55365	0.7	0.831389
	Target:  5'- cGGACAcauCCAGUcuaucACGGAGGG-UUCUCg -3' miRNA:   3'- aCCUGU---GGUCAu----UGCCUCUUgAAGAG- -5'
22159	5'	-49.9	NC_004927.1	+	32097	0.69	0.889666
	Target:  5'- gGGACGUagaAGUAgGCGGGGAAgUUCUCc -3' miRNA:   3'- aCCUGUGg--UCAU-UGCCUCUUgAAGAG- -5'
22159	5'	-49.9	NC_004927.1	+	8605	0.68	0.934738
	Target:  5'- cGaGGCuCCGGUAGCguucguggguguGGAGAGCUUCg- -3' miRNA:   3'- aC-CUGuGGUCAUUG------------CCUCUUGAAGag -5'
22159	5'	-49.9	NC_004927.1	+	50288	0.67	0.940032
	Target:  5'- gGGAgUGCCGGUAACGGAGuGACa---- -3' miRNA:   3'- aCCU-GUGGUCAUUGCCUC-UUGaagag -5'
22159	5'	-49.9	NC_004927.1	+	60990	0.67	0.943568
	Target:  5'- gUGaGugACCAG-AACGGAGAugaggcggguauccGCUUCg- -3' miRNA:   3'- -AC-CugUGGUCaUUGCCUCU--------------UGAAGag -5'
22159	5'	-49.9	NC_004927.1	+	30003	0.66	0.975367
	Target:  5'- cGGA-AUCAGgcagGACGGAGGaacGCUUcCUCa -3' miRNA:   3'- aCCUgUGGUCa---UUGCCUCU---UGAA-GAG- -5'
22159	5'	-49.9	NC_004927.1	+	55325	0.66	0.975367
	Target:  5'- aUGGACAa----GACGGAGGACaaUCUCa -3' miRNA:   3'- -ACCUGUggucaUUGCCUCUUGa-AGAG- -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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