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
668	5'	-59.7	AC_000018.1	+	27202	0.66	0.363751
	Target:  5'- gGGAGUuuCCUGGUacacCAGGGCGGcgGGCc -3' miRNA:   3'- gCCUCG--GGGCCGau--GUCUCGCUa-CCG- -5'
668	5'	-59.7	AC_000018.1	+	28191	0.68	0.277611
	Target:  5'- gCGGAGCUcaccuCCGGuUUugGGAGUGGuaguauUGGCa -3' miRNA:   3'- -GCCUCGG-----GGCC-GAugUCUCGCU------ACCG- -5'
668	5'	-59.7	AC_000018.1	+	9706	0.69	0.242277
	Target:  5'- aGGAGCaccaggucuuugggUCCGGCUuguuggaugcGCAG-GCGAUGGg -3' miRNA:   3'- gCCUCG--------------GGGCCGA----------UGUCuCGCUACCg -5'
668	5'	-59.7	AC_000018.1	+	18487	0.69	0.236662
	Target:  5'- gCGGuguGCCCCcaggacgcggucuGGCUACGGcaacgggcuguacGGCGGUGGg -3' miRNA:   3'- -GCCu--CGGGG-------------CCGAUGUC-------------UCGCUACCg -5'
668	5'	-59.7	AC_000018.1	+	14142	0.72	0.138603
	Target:  5'- aGGAGacgagCCGuGCUagGCGGAGCGGUGGUg -3' miRNA:   3'- gCCUCgg---GGC-CGA--UGUCUCGCUACCG- -5'
668	5'	-59.7	AC_000018.1	+	10186	0.72	0.133678
	Target:  5'- cCGGGGCUCCGGggGCAaggucuuccagcauGAgGCGGUGGUa -3' miRNA:   3'- -GCCUCGGGGCCgaUGU--------------CU-CGCUACCG- -5'
668	5'	-59.7	AC_000018.1	+	10232	1.1	0.000166
	Target:  5'- cCGGAGCCCCGGCUACAGAGCGAUGGCc -3' miRNA:   3'- -GCCUCGGGGCCGAUGUCUCGCUACCG- -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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