miRNA: 3'- uaagCUCAGUGa-----UgCAGUUGCGG-UCG- -5'
miRNA: 3'- uaaGC-UC-AGUGAUGCAGUUG-------CGGUCG- -5'
miRNA: 3'- uaAGCUC---AGUGaUGCAGUUGCGGUCG- -5'
miRNA: 3'- -UAAGCUCAGUGAUGCAGUUGCGGUCG- -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 | |||||||
| 32562 | 3' | -50.7 | NC_007149.1 | + | 15732 | 0.66 | 0.835857 |
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Target: 5'- ---gGAGUUACaccuaaAgGUCAACGCCgAGCa -3' miRNA: 3'- uaagCUCAGUGa-----UgCAGUUGCGG-UCG- -5' |
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| 32562 | 3' | -50.7 | NC_007149.1 | + | 22052 | 0.75 | 0.359467 |
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Target: 5'- --gCGuAGuUCGCUACGUCAGCagccauaGCCAGCg -3' miRNA: 3'- uaaGC-UC-AGUGAUGCAGUUG-------CGGUCG- -5' |
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| 32562 | 3' | -50.7 | NC_007149.1 | + | 22961 | 0.8 | 0.18824 |
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Target: 5'- -gUCGAGcguUCACaACGUCAGCGUUAGCa -3' miRNA: 3'- uaAGCUC---AGUGaUGCAGUUGCGGUCG- -5' |
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| 32562 | 3' | -50.7 | NC_007149.1 | + | 35713 | 1.12 | 0.001255 |
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Target: 5'- gAUUCGAGUCACUACGUCAACGCCAGCa -3' miRNA: 3'- -UAAGCUCAGUGAUGCAGUUGCGGUCG- -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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