miRNA: 3'- cCGCGCGa---GUGGGU------UGAGGAGUUGaa -5'
miRNA: 3'- -CCGCGCgA--------GUGGGUuGAGGAGu--UGAa -5'
miRNA: 3'- cCGCGCGAGUGGGUU-GAGGAG---UUGAa -5'
miRNA: 3'- -CCGCGCGAGUGGGUUGAGGAGUUGAA- -5'
Results 1 - 4 of 4 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand | Start Position | R_P_ratio# |
P value
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| Predicted miRNA align pattern | |||||||
| 7473 | 5' | -55.5 | NC_001918.1 | + | 5365 | 0.68 | 0.134142 |
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Target: 5'- aGCGCGCcgcgCGCUCGaugggcGCUCUUCGACg- -3' miRNA: 3'- cCGCGCGa---GUGGGU------UGAGGAGUUGaa -5' |
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| 7473 | 5' | -55.5 | NC_001918.1 | + | 2619 | 0.68 | 0.125692 |
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Target: 5'- uGGCGCGgUgaacucgcCGCCCAcCUCCUCuucACUg -3' miRNA: 3'- -CCGCGCgA--------GUGGGUuGAGGAGu--UGAa -5' |
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| 7473 | 5' | -55.5 | NC_001918.1 | + | 1919 | 0.78 | 0.018203 |
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Target: 5'- uGCGUGCUUACCCAGaCUCCUCcugGGCUg -3' miRNA: 3'- cCGCGCGAGUGGGUU-GAGGAG---UUGAa -5' |
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| 7473 | 5' | -55.5 | NC_001918.1 | + | 1146 | 1.07 | 7.4e-05 |
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Target: 5'- gGGCGCGCUCACCCAACUCCUCAACUUc -3' miRNA: 3'- -CCGCGCGAGUGGGUUGAGGAGUUGAA- -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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