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
13067	3'	-49.8	NC_003390.1	+	21807	0.66	0.903646
	Target:  5'- uGGGCAacagaGUGGGAgagaUCUgGAUGGUc -3' miRNA:   3'- uCCCGU-----UAUCCUaaggAGAgUUACCG- -5'
13067	3'	-49.8	NC_003390.1	+	28161	0.67	0.880867
	Target:  5'- cAGuGGCAGUcg---UCCUCUCGGacUGGCg -3' miRNA:   3'- -UC-CCGUUAuccuaAGGAGAGUU--ACCG- -5'
13067	3'	-49.8	NC_003390.1	+	39824	0.67	0.864237
	Target:  5'- cGGGCAcagaAGGA--CUUCUUAcgGGCa -3' miRNA:   3'- uCCCGUua--UCCUaaGGAGAGUuaCCG- -5'
13067	3'	-49.8	NC_003390.1	+	13747	0.68	0.855511
	Target:  5'- uAGGuGCGGUGGGuuugucgUCCUCgaaaUCGAgGGCu -3' miRNA:   3'- -UCC-CGUUAUCCua-----AGGAG----AGUUaCCG- -5'
13067	3'	-49.8	NC_003390.1	+	7003	0.7	0.744654
	Target:  5'- cAGGGCAGUcagccacugGGGAUaCCaUUCGggGGCa -3' miRNA:   3'- -UCCCGUUA---------UCCUAaGGaGAGUuaCCG- -5'
13067	3'	-49.8	NC_003390.1	+	17001	0.73	0.583533
	Target:  5'- gAGG--AAUGGGAUcuUCCgcagCUCAAUGGCg -3' miRNA:   3'- -UCCcgUUAUCCUA--AGGa---GAGUUACCG- -5'
13067	3'	-49.8	NC_003390.1	+	21693	1.12	0.001812
	Target:  5'- uAGGGCAAUAGGAUUCCUCUCAAUGGCc -3' miRNA:   3'- -UCCCGUUAUCCUAAGGAGAGUUACCG- -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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