miRNA: 3'- -GAGa---AGGAGCUGcaaCUUGUCUAGGa -5'
miRNA: 3'- gAGaa-GGa-GCUGCAac-UUGUCUAGGa -5'
miRNA: 3'- -GAGa------AGGaGCUGCAACUUGUCu-------AGGa -5'
miRNA: 3'- -GAGAAGGAGCUGCAACUUGUCUAGGA- -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 | |||||||
| 18565 | 5' | -49.4 | NC_004682.1 | + | 32199 | 0.66 | 0.951894 |
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Target: 5'- gCUCguccUUCUUGACcgaGAGCAGGUCCa -3' miRNA: 3'- -GAGa---AGGAGCUGcaaCUUGUCUAGGa -5' |
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| 18565 | 5' | -49.4 | NC_004682.1 | + | 24450 | 0.66 | 0.947183 |
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Target: 5'- uUCgacCCggCGACGUggaAGCAGAUCCa -3' miRNA: 3'- gAGaa-GGa-GCUGCAac-UUGUCUAGGa -5' |
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| 18565 | 5' | -49.4 | NC_004682.1 | + | 34860 | 0.67 | 0.925362 |
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Target: 5'- cCUCguugggcUCCcCGACGUUGGACAGcgacgaguUCCa -3' miRNA: 3'- -GAGa------AGGaGCUGCAACUUGUCu-------AGGa -5' |
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| 18565 | 5' | -49.4 | NC_004682.1 | + | 35724 | 1.08 | 0.00439 |
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Target: 5'- cCUCUUCCUCGACGUUGAACAGAUCCUc -3' miRNA: 3'- -GAGAAGGAGCUGCAACUUGUCUAGGA- -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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