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
21821	3'	-55	NC_004831.2	+	43301	0.65	0.665751
	Target:  5'- -aGCCUUCUCCuugauaGACUUCACuaaUGGCa -3' miRNA:   3'- caCGGAAGAGG------UUGAGGUGug-GUCGc -5'
21821	3'	-55	NC_004831.2	+	31688	0.66	0.62052
	Target:  5'- aGUGCCUUCuucuuaacaUCCAAgUCUAgccUAUCAGCa -3' miRNA:   3'- -CACGGAAG---------AGGUUgAGGU---GUGGUCGc -5'
21821	3'	-55	NC_004831.2	+	38765	0.67	0.553181
	Target:  5'- cUGCCUugUCUCCAuCUUCAggUGCCAGUa -3' miRNA:   3'- cACGGA--AGAGGUuGAGGU--GUGGUCGc -5'
21821	3'	-55	NC_004831.2	+	39374	0.68	0.54214
	Target:  5'- aUGCCUuagcaaccaucuUCUCaCAccauGCaaugcaguuaUCCACGCCAGCGa -3' miRNA:   3'- cACGGA------------AGAG-GU----UG----------AGGUGUGGUCGC- -5'
21821	3'	-55	NC_004831.2	+	20353	0.7	0.407636
	Target:  5'- uUGCCUuugCUCCAGCgccUUCAUugCAGUGg -3' miRNA:   3'- cACGGAa--GAGGUUG---AGGUGugGUCGC- -5'
21821	3'	-55	NC_004831.2	+	961	0.73	0.273881
	Target:  5'- aGUGCCUUgauaggCCAGC-CUACGCCAGCc -3' miRNA:   3'- -CACGGAAga----GGUUGaGGUGUGGUCGc -5'
21821	3'	-55	NC_004831.2	+	16954	1.1	0.000601
	Target:  5'- cGUGCCUUCUCCAACUCCACACCAGCGg -3' miRNA:   3'- -CACGGAAGAGGUUGAGGUGUGGUCGC- -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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