miRNA: 3'- -AAGUAGGCCAGUCGGACCGACUGGCC- -5'
miRNA: 3'- aAGUaGGCCAGUCGGaCCGACUGGCC- -5'
miRNA: 3'- aAGUaGGCCAG--UCG-GaCCGACUGGCc -5'
miRNA: 3'- -AAGUAGG------CCAGUCGGACCGaCUGgCc -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 | |||||||
| 22440 | 5' | -58.4 | NC_005056.1 | + | 17542 | 1.07 | 0.000305 |
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Target: 5'- uUUCAUCCGGUCAGCCUGGCUGACCGGu -3' miRNA: 3'- -AAGUAGGCCAGUCGGACCGACUGGCC- -5' |
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| 22440 | 5' | -58.4 | NC_005056.1 | + | 17605 | 0.88 | 0.008804 |
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Target: 5'- gUUAaCCGGUCAGCCaGGCUGACCGGa -3' miRNA: 3'- aAGUaGGCCAGUCGGaCCGACUGGCC- -5' |
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| 22440 | 5' | -58.4 | NC_005056.1 | + | 20277 | 0.7 | 0.203046 |
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Target: 5'- aUCAgCCGGUCacGGCaCcGGCUGGCCGc -3' miRNA: 3'- aAGUaGGCCAG--UCG-GaCCGACUGGCc -5' |
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| 22440 | 5' | -58.4 | NC_005056.1 | + | 28346 | 0.66 | 0.395329 |
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Target: 5'- aUUCGUUCcgaccgGGUCAGUCUGGCcGACgGu -3' miRNA: 3'- -AAGUAGG------CCAGUCGGACCGaCUGgCc -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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