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
234	3'	-56.8	AC_000008.1	+	8537	0.66	0.534916
	Target:  5'- cGGGCGGUgggCC-GCGGGgGUGuCCUu- -3' miRNA:   3'- cCCCGCUAa--GGaCGUCCgCAU-GGAcg -5'
234	3'	-56.8	AC_000008.1	+	17260	0.67	0.441064
	Target:  5'- cGGuGGCGGaugCCgcggUGCAGGCGgucgCUGCg -3' miRNA:   3'- -CC-CCGCUaa-GG----ACGUCCGCaug-GACG- -5'
234	3'	-56.8	AC_000008.1	+	27458	0.7	0.285306
	Target:  5'- aGGGGCGcagCUUGCGGGCG-GCUuucgucacagggUGCg -3' miRNA:   3'- -CCCCGCuaaGGACGUCCGCaUGG------------ACG- -5'
234	3'	-56.8	AC_000008.1	+	12096	0.71	0.257187
	Target:  5'- -cGGCGAUagagaggccgagUCCUacuuugacGCGGGCGcugACCUGCg -3' miRNA:   3'- ccCCGCUA------------AGGA--------CGUCCGCa--UGGACG- -5'
234	3'	-56.8	AC_000008.1	+	8387	0.74	0.153391
	Target:  5'- -aGGCGGgagcUCCUGCAGGUuUACCUcGCa -3' miRNA:   3'- ccCCGCUa---AGGACGUCCGcAUGGA-CG- -5'
234	3'	-56.8	AC_000008.1	+	24005	0.75	0.13704
	Target:  5'- aGGGGUauGGUauaUCUUGCGGGCGUaaaACUUGCc -3' miRNA:   3'- -CCCCG--CUA---AGGACGUCCGCA---UGGACG- -5'
234	3'	-56.8	AC_000008.1	+	12625	1.14	0.000174
	Target:  5'- uGGGGCGAUUCCUGCAGGCGUACCUGCa -3' miRNA:   3'- -CCCCGCUAAGGACGUCCGCAUGGACG- -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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