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ID | Location | Perfect MFE.* | RefSeq Acc. | strand | Start Position | R_P_ratio# | P value |
Predicted miRNA align pattern | |||||||
8880 | 3' | -54.1 | NC_002484.1 | + | 32701 | 0.69 | 0.630548 |
Target: 5'- uGCGCGAUGcGCUgcuggccuUCGcGAAGAacgCCCCa -3' miRNA: 3'- cCGCGCUACuUGA--------GGC-CUUCUa--GGGG- -5' |
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8880 | 3' | -54.1 | NC_002484.1 | + | 16652 | 0.66 | 0.817265 |
Target: 5'- cGGgGUGAgauugGAGCUCuCGGucAGGUCCaggCCg -3' miRNA: 3'- -CCgCGCUa----CUUGAG-GCCu-UCUAGG---GG- -5' |
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8880 | 3' | -54.1 | NC_002484.1 | + | 319 | 0.69 | 0.663296 |
Target: 5'- aGGUucGCGGUGAcCUCCaGGAuGAUCCgguCCg -3' miRNA: 3'- -CCG--CGCUACUuGAGG-CCUuCUAGG---GG- -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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