miRNA: 3'- uCGACGGGu--CU-------UUCUUGuua--AACGGC- -5'
miRNA: 3'- -UCGACGGg-UCUUUCu----UGUUa-AACGGC- -5'
miRNA: 3'- -UCGACGGGUCuuu-CUugUUaaACGGC- -5'
miRNA: 3'- -UCGACGGGUCUUUCUUGUUAAACGGC- -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 | |||||||
| 22821 | 5' | -48.8 | NC_005135.1 | + | 167905 | 0.65 | 0.999312 |
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Target: 5'- uGCUGCCUguuGAaccauacGAGAACcgaagUUGCCGu -3' miRNA: 3'- uCGACGGGu--CU-------UUCUUGuua--AACGGC- -5' |
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| 22821 | 5' | -48.8 | NC_005135.1 | + | 61580 | 0.67 | 0.997381 |
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Target: 5'- aAGCUGCUgaAGAAGGuucgcGCGAacUUGCCGa -3' miRNA: 3'- -UCGACGGg-UCUUUCu----UGUUa-AACGGC- -5' |
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| 22821 | 5' | -48.8 | NC_005135.1 | + | 170413 | 0.68 | 0.99315 |
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Target: 5'- cGGCUGCCCAGcgguGAugAAa-UGCUGu -3' miRNA: 3'- -UCGACGGGUCuuu-CUugUUaaACGGC- -5' |
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| 22821 | 5' | -48.8 | NC_005135.1 | + | 27093 | 1.11 | 0.01063 |
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Target: 5'- cAGCUGCCCAGAAAGAACAAUUUGCCGg -3' miRNA: 3'- -UCGACGGGUCUUUCUUGUUAAACGGC- -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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