miRNA: 3'- uagUAUUAGUGG-UAGCCG-----------UCCGACga -5'
miRNA: 3'- -UAGuau-UAGUGGuaGCCGUCCGaCGA- -5'
miRNA: 3'- -UAGUAUUAGUGG--------UAGcCGUCCGA-CGa -5'
miRNA: 3'- -UAGUAUU---AGUGGUAGCCGUCCG----ACGa -5'
miRNA: 3'- -UAGUAUUAGUGGUAGCCGUCCGACGA- -5'
Results 1 - 5 of 5 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 | |||||||
| 17500 | 3' | -52.6 | NC_004456.1 | + | 35305 | 0.67 | 0.694808 |
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Target: 5'- --aGUGGUCGCCuAUCGGCuugaugaugaaGGGCUGg- -3' miRNA: 3'- uagUAUUAGUGG-UAGCCG-----------UCCGACga -5' |
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| 17500 | 3' | -52.6 | NC_004456.1 | + | 27521 | 0.67 | 0.660048 |
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Target: 5'- uAUCuggcGUCAUCggCGGCGGGCgGCUc -3' miRNA: 3'- -UAGuau-UAGUGGuaGCCGUCCGaCGA- -5' |
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| 17500 | 3' | -52.6 | NC_004456.1 | + | 31245 | 0.68 | 0.636707 |
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Target: 5'- gGUCGUGGUCACUuccuucgcGUCaGCAGGUUgGCa -3' miRNA: 3'- -UAGUAUUAGUGG--------UAGcCGUCCGA-CGa -5' |
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| 17500 | 3' | -52.6 | NC_004456.1 | + | 28133 | 0.74 | 0.275835 |
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Target: 5'- aGUCGUGAcuaUCGUCAUCGGCAGGCccguUGCg -3' miRNA: 3'- -UAGUAUU---AGUGGUAGCCGUCCG----ACGa -5' |
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| 17500 | 3' | -52.6 | NC_004456.1 | + | 6780 | 1.05 | 0.00182 |
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Target: 5'- cAUCAUAAUCACCAUCGGCAGGCUGCUc -3' miRNA: 3'- -UAGUAUUAGUGGUAGCCGUCCGACGA- -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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