miRNA: 3'- aCGu-GCGGuCUGAAAGUUG---------------CCGCC-CU- -5'
miRNA: 3'- aCGUG----CGGUCUGa------------AAGUUGCCGCC-CU- -5'
miRNA: 3'- -ACGUGCGGUCUGAAAGUUGCCGCCCU- -5'
miRNA: 3'- -ACGUGCGGUCUGAAAGUUGCCGCCCU- -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 | |||||||
| 27297 | 5' | -55.3 | NC_005856.1 | + | 20390 | 0.67 | 0.809598 |
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Target: 5'- aGCucCGCC-GACUUUCGACaaugaaguuaucgcuGGCGGcGAu -3' miRNA: 3'- aCGu-GCGGuCUGAAAGUUG---------------CCGCC-CU- -5' |
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| 27297 | 5' | -55.3 | NC_005856.1 | + | 26402 | 0.69 | 0.639359 |
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Target: 5'- aGCACcaggGCCAGGCgcugggggauaugUUUGGCGGCGGcGAu -3' miRNA: 3'- aCGUG----CGGUCUGa------------AAGUUGCCGCC-CU- -5' |
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| 27297 | 5' | -55.3 | NC_005856.1 | + | 32258 | 1.09 | 0.001873 |
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Target: 5'- gUGCACGCCAGACUUUCAACGGCGGGAu -3' miRNA: 3'- -ACGUGCGGUCUGAAAGUUGCCGCCCU- -5' |
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| 27297 | 5' | -55.3 | NC_005856.1 | + | 36473 | 1.09 | 0.001873 |
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Target: 5'- gUGCACGCCAGACUUUCAACGGCGGGAu -3' miRNA: 3'- -ACGUGCGGUCUGAAAGUUGCCGCCCU- -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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