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
17653	3'	-61.1	NC_004466.2	+	40294	0.66	0.357048
	Target:  5'- gACCGGcacCCAGGGCGcUAGCcgagguugaAUCCGAGg -3' miRNA:   3'- -UGGUCu--GGUCCCGUcGUCG---------UGGGCUC- -5'
17653	3'	-61.1	NC_004466.2	+	17097	0.66	0.340549
	Target:  5'- --aGGAgUGGGGCAGCgauaacaccAGCACCCGcAGu -3' miRNA:   3'- uggUCUgGUCCCGUCG---------UCGUGGGC-UC- -5'
17653	3'	-61.1	NC_004466.2	+	44871	0.67	0.280159
	Target:  5'- gGCCAgGGCCAGccGGCGGgAGC-CuuGAGg -3' miRNA:   3'- -UGGU-CUGGUC--CCGUCgUCGuGggCUC- -5'
17653	3'	-61.1	NC_004466.2	+	44981	0.71	0.149384
	Target:  5'- aACCAGcuuguCCAGGGCAGCA-C-CCCGGu -3' miRNA:   3'- -UGGUCu----GGUCCCGUCGUcGuGGGCUc -5'
17653	3'	-61.1	NC_004466.2	+	35465	0.73	0.116643
	Target:  5'- -aCAG-CCAGGGCAGCAGCcgccagACCCa-- -3' miRNA:   3'- ugGUCuGGUCCCGUCGUCG------UGGGcuc -5'
17653	3'	-61.1	NC_004466.2	+	39190	0.73	0.104349
	Target:  5'- uACCAGACCuccGGGGUAGUGGU-CCUGGGg -3' miRNA:   3'- -UGGUCUGG---UCCCGUCGUCGuGGGCUC- -5'
17653	3'	-61.1	NC_004466.2	+	34581	1.08	0.000216
	Target:  5'- cACCAGACCAGGGCAGCAGCACCCGAGa -3' miRNA:   3'- -UGGUCUGGUCCCGUCGUCGUGGGCUC- -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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