miRNA: 3'- caGGCA-GUCGUUGUGCgAUCuGUCGu -5'
miRNA: 3'- -CAGGCAG---UCGUUGUGCGa-UCUGUCgu -5'
miRNA: 3'- caGGCAGUCGU-----UGUGCGaUCuGUCGu -5'
miRNA: 3'- -CAGGCAGUCGUUGUGCGAUCUGUCGU- -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 | |||||||
| 14705 | 5' | -53.5 | NC_003529.1 | + | 129291 | 0.66 | 0.947389 |
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Target: 5'- -aCCGUcCGGCAACGCGgUGG-UAGUg -3' miRNA: 3'- caGGCA-GUCGUUGUGCgAUCuGUCGu -5' |
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| 14705 | 5' | -53.5 | NC_003529.1 | + | 88950 | 0.66 | 0.947389 |
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Target: 5'- uGUCUGUUucgAGCAGCGCGUcaAGGCAGa- -3' miRNA: 3'- -CAGGCAG---UCGUUGUGCGa-UCUGUCgu -5' |
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| 14705 | 5' | -53.5 | NC_003529.1 | + | 33164 | 0.69 | 0.853108 |
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Target: 5'- -gCCGUCGGCAaaagcGCACGC-GGcCAGCc -3' miRNA: 3'- caGGCAGUCGU-----UGUGCGaUCuGUCGu -5' |
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| 14705 | 5' | -53.5 | NC_003529.1 | + | 68067 | 1.08 | 0.00501 |
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Target: 5'- gGUCCGUCAGCAACACGCUAGACAGCAc -3' miRNA: 3'- -CAGGCAGUCGUUGUGCGAUCUGUCGU- -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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