miRNA: 3'- -UCUGAGCUGUCa------GGCUCG-GC--------------AGCGau -5'
miRNA: 3'- ucUGAGCUGUc----AGGCu-CGGCAGCGAU- -5'
miRNA: 3'- -UCUGaGCUGUCaG-GCUCGGCAGCGau -5'
miRNA: 3'- -UCUGAGCUGUCAGGCUCGGCAGCGAU- -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 | |||||||
| 27568 | 3' | -57.1 | NC_005882.1 | + | 15973 | 0.66 | 0.457025 |
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Target: 5'- cGGAUUCGGCAGguacaugCCGAGCgCGaagaaaucaaugcuUCGCg- -3' miRNA: 3'- -UCUGAGCUGUCa------GGCUCG-GC--------------AGCGau -5' |
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| 27568 | 3' | -57.1 | NC_005882.1 | + | 19309 | 0.67 | 0.449965 |
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Target: 5'- -aACUCGACGacgccUUCGuuGCCGUCGCUGa -3' miRNA: 3'- ucUGAGCUGUc----AGGCu-CGGCAGCGAU- -5' |
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| 27568 | 3' | -57.1 | NC_005882.1 | + | 25453 | 0.68 | 0.373856 |
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Target: 5'- gGGACgCGAUGG-CgCGGGCCGUUGCg- -3' miRNA: 3'- -UCUGaGCUGUCaG-GCUCGGCAGCGau -5' |
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| 27568 | 3' | -57.1 | NC_005882.1 | + | 7343 | 1.06 | 0.000582 |
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Target: 5'- gAGACUCGACAGUCCGAGCCGUCGCUAc -3' miRNA: 3'- -UCUGAGCUGUCAGGCUCGGCAGCGAU- -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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