miRNA: 3'- uaCGACGGUGgauaGUUCU--AAACGUU- -5'
miRNA: 3'- uACGACGGUGGa-------UAGUucUAAACGUU- -5'
miRNA: 3'- -UACGA---CGGUGGAua-----------GUUCUAAACGUU- -5'
miRNA: 3'- -UACGACGGUGGAUAGUUCUAAACGUU- -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 | |||||||
| 17363 | 5' | -49.4 | NC_004367.1 | + | 114514 | 0.66 | 0.991636 |
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Target: 5'- -aGCUGCCAUa---CAAGAaaUUUGCAGa -3' miRNA: 3'- uaCGACGGUGgauaGUUCU--AAACGUU- -5' |
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| 17363 | 5' | -49.4 | NC_004367.1 | + | 74939 | 0.68 | 0.979114 |
|
Target: 5'- uUGUUGCCACCggcuggcaAUCA--GUUUGCAAg -3' miRNA: 3'- uACGACGGUGGa-------UAGUucUAAACGUU- -5' |
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| 17363 | 5' | -49.4 | NC_004367.1 | + | 35505 | 0.7 | 0.944502 |
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Target: 5'- aGUGCUgacGCCGCCUcuuauuucuauggCGGGGUUUGCAAa -3' miRNA: 3'- -UACGA---CGGUGGAua-----------GUUCUAAACGUU- -5' |
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| 17363 | 5' | -49.4 | NC_004367.1 | + | 74710 | 1.05 | 0.014478 |
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Target: 5'- cAUGCUGCCACCUAUCAAGAUUUGCAAg -3' miRNA: 3'- -UACGACGGUGGAUAGUUCUAAACGUU- -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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