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
21390	3'	-65.8	NC_004812.1	+	45	0.77	0.099374
	Target:  5'- cGGCGggccGCGGGCGCGGCGGCgCGGcGCc -3' miRNA:   3'- aCCGC----UGCCUGUGCCGCCG-GCCcCGc -5'
21390	3'	-65.8	NC_004812.1	+	93	0.69	0.330099
	Target:  5'- aGG-GACGGGCcGgGGCGcGCgCGGGGCc -3' miRNA:   3'- aCCgCUGCCUG-UgCCGC-CG-GCCCCGc -5'
21390	3'	-65.8	NC_004812.1	+	508	0.71	0.266173
	Target:  5'- ----cACGGcCGCcGCGGCCGGGGCGg -3' miRNA:   3'- accgcUGCCuGUGcCGCCGGCCCCGC- -5'
21390	3'	-65.8	NC_004812.1	+	683	0.68	0.395947
	Target:  5'- cGGCGcucccGCGGcccggccuccucgGCGCGGCaGCCcGGGCGc -3' miRNA:   3'- aCCGC-----UGCC-------------UGUGCCGcCGGcCCCGC- -5'
21390	3'	-65.8	NC_004812.1	+	722	0.73	0.189518
	Target:  5'- cGGCGcCGG-CGCGGUcgccGGCgGGGGUGg -3' miRNA:   3'- aCCGCuGCCuGUGCCG----CCGgCCCCGC- -5'
21390	3'	-65.8	NC_004812.1	+	791	0.67	0.445704
	Target:  5'- gGGCcuCGGGuucgcuuccgccCACGGcCGGCCGGGaaGCGg -3' miRNA:   3'- aCCGcuGCCU------------GUGCC-GCCGGCCC--CGC- -5'
21390	3'	-65.8	NC_004812.1	+	1087	0.66	0.504139
	Target:  5'- cGGCcGCGGucuccuccuGCcCGGCGGCCcgggucgcuucgccGGGGCc -3' miRNA:   3'- aCCGcUGCC---------UGuGCCGCCGG--------------CCCCGc -5'
21390	3'	-65.8	NC_004812.1	+	1212	0.67	0.429001
	Target:  5'- cGGC--CGGGgGCGGCGccGCgGGGGCu -3' miRNA:   3'- aCCGcuGCCUgUGCCGC--CGgCCCCGc -5'
21390	3'	-65.8	NC_004812.1	+	1268	0.66	0.524052
	Target:  5'- -uGCGACGGGCAgauucCGGCccccaggguccccGGaggCGGGGCGc -3' miRNA:   3'- acCGCUGCCUGU-----GCCG-------------CCg--GCCCCGC- -5'
21390	3'	-65.8	NC_004812.1	+	1279	0.76	0.11785
	Target:  5'- cGGCcGCGGGCG-GGCGGuCCGaGGGCGg -3' miRNA:   3'- aCCGcUGCCUGUgCCGCC-GGC-CCCGC- -5'
21390	3'	-65.8	NC_004812.1	+	1312	0.72	0.238153
	Target:  5'- gGGCGguccGCGGGCgguccGCgGGCGGuCCGcGGGCGg -3' miRNA:   3'- aCCGC----UGCCUG-----UG-CCGCC-GGC-CCCGC- -5'
21390	3'	-65.8	NC_004812.1	+	1414	0.71	0.249054
	Target:  5'- cGGCcccgacGGCGGcCGCGGggaggGGCCGGGGCc -3' miRNA:   3'- aCCG------CUGCCuGUGCCg----CCGGCCCCGc -5'
21390	3'	-65.8	NC_004812.1	+	1467	0.74	0.157113
	Target:  5'- cGGCGACGccGGCGuccuCGGCGGgCGGcGGCGg -3' miRNA:   3'- aCCGCUGC--CUGU----GCCGCCgGCC-CCGC- -5'
21390	3'	-65.8	NC_004812.1	+	1904	0.67	0.462765
	Target:  5'- -cGCGGCaccccguauauGGGCcgaGGCuccGGCCGGGGCGc -3' miRNA:   3'- acCGCUG-----------CCUGug-CCG---CCGGCCCCGC- -5'
21390	3'	-65.8	NC_004812.1	+	1992	0.74	0.157113
	Target:  5'- gGGUGGCGGGuccCGcCGGCGGUcgcuCGGGGCGc -3' miRNA:   3'- aCCGCUGCCU---GU-GCCGCCG----GCCCCGC- -5'
21390	3'	-65.8	NC_004812.1	+	2050	0.79	0.075769
	Target:  5'- cGGCGGgGGGCGCGGgGGagGGGGCGc -3' miRNA:   3'- aCCGCUgCCUGUGCCgCCggCCCCGC- -5'
21390	3'	-65.8	NC_004812.1	+	2165	0.7	0.315788
	Target:  5'- cGGCGGCGGccaccucCACGGCGG-CGGcgucgucgucgucGGCGa -3' miRNA:   3'- aCCGCUGCCu------GUGCCGCCgGCC-------------CCGC- -5'
21390	3'	-65.8	NC_004812.1	+	2237	0.69	0.351363
	Target:  5'- -aGCGcacGCGcGGCGCGGCGGCgGGGuccGCGu -3' miRNA:   3'- acCGC---UGC-CUGUGCCGCCGgCCC---CGC- -5'
21390	3'	-65.8	NC_004812.1	+	2357	0.67	0.445704
	Target:  5'- gGGCGuCGGGCcCGGCGcGCgCGGcgucGCGg -3' miRNA:   3'- aCCGCuGCCUGuGCCGC-CG-GCCc---CGC- -5'
21390	3'	-65.8	NC_004812.1	+	2480	0.75	0.146309
	Target:  5'- gGGCGcCGGcgGCGGCGGCCucgcGGGCGg -3' miRNA:   3'- aCCGCuGCCugUGCCGCCGGc---CCCGC- -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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