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
680	3'	-56.6	AC_000018.1	+	12665	0.66	0.496608
	Target:  5'- uCUCAGCGCgagcggUUCC-AGCGCggcgCCAacuUGGg -3' miRNA:   3'- cGGGUCGCG------AAGGuUCGCGa---GGU---ACC- -5'
680	3'	-56.6	AC_000018.1	+	22828	0.66	0.485008
	Target:  5'- cCCCAGCGgUUCUggGUgaucuugGCUCUGucUGGg -3' miRNA:   3'- cGGGUCGCgAAGGuuCG-------CGAGGU--ACC- -5'
680	3'	-56.6	AC_000018.1	+	12734	0.67	0.465283
	Target:  5'- aCCCAGC-CcgCCAAcGUGCcCCGUGGu -3' miRNA:   3'- cGGGUCGcGaaGGUU-CGCGaGGUACC- -5'
680	3'	-56.6	AC_000018.1	+	23062	0.67	0.44498
	Target:  5'- cGCCCAcaauaguugggaGUGCa-CCGgguGCGCUCUGUGGg -3' miRNA:   3'- -CGGGU------------CGCGaaGGUu--CGCGAGGUACC- -5'
680	3'	-56.6	AC_000018.1	+	8032	0.69	0.360245
	Target:  5'- gGCCUGGCGUUUguaCCuGGCGCUCUAc-- -3' miRNA:   3'- -CGGGUCGCGAA---GGuUCGCGAGGUacc -5'
680	3'	-56.6	AC_000018.1	+	5125	0.74	0.15406
	Target:  5'- cGUCCAGCGCUgCCAGG-GUccgauccuUCCAUGGu -3' miRNA:   3'- -CGGGUCGCGAaGGUUCgCG--------AGGUACC- -5'
680	3'	-56.6	AC_000018.1	+	9032	1.12	0.00025
	Target:  5'- cGCCCAGCGCUUCCAAGCGCUCCAUGGc -3' miRNA:   3'- -CGGGUCGCGAAGGUUCGCGAGGUACC- -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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