miRNA: 3'- gaCCACUGGC---------CgACGUCGA---------CUUGGAC- -5'
miRNA: 3'- -GACCACUg--GCCGACGu-----CGACU--UGGac -5'
miRNA: 3'- -GACC-ACUGGC---CGACgUCGaCUUGGAC- -5'
miRNA: 3'- -GACCACUGGCCGACGUCGACUUGGAC- -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 | |||||||
| 27367 | 3' | -57.4 | NC_005857.1 | + | 32351 | 0.66 | 0.562019 |
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Target: 5'- -gGGUGGCCGcaugaaucaGgUGCAGCUaaacacccaGGGCCUGc -3' miRNA: 3'- gaCCACUGGC---------CgACGUCGA---------CUUGGAC- -5' |
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| 27367 | 3' | -57.4 | NC_005857.1 | + | 11887 | 0.67 | 0.508639 |
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Target: 5'- cCUGGUGGauaUGGCUGCucaggcGCUGGuuACCa- -3' miRNA: 3'- -GACCACUg--GCCGACGu-----CGACU--UGGac -5' |
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| 27367 | 3' | -57.4 | NC_005857.1 | + | 8878 | 0.72 | 0.257462 |
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Target: 5'- uCUGGcUGGCCGaccGCUGgGGC-GAGCCUGa -3' miRNA: 3'- -GACC-ACUGGC---CGACgUCGaCUUGGAC- -5' |
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| 27367 | 3' | -57.4 | NC_005857.1 | + | 16867 | 1.07 | 0.000654 |
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Target: 5'- gCUGGUGACCGGCUGCAGCUGAACCUGc -3' miRNA: 3'- -GACCACUGGCCGACGUCGACUUGGAC- -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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