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miRNA: 3'- -UCCCAG-----AAGU------GGUGCUCGCCUCagGC- -5'
miRNA: 3'- uccCAgAAGuGGUGCU--CGCCUCAGGc -5'
miRNA: 3'- uCCCAgAAGug-GUGCUCG-CC-UCAGGc -5'
miRNA: 3'- ucCCAGaAGUGGUGCU-CGCCucAGGC- -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#
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P value |
| Predicted miRNA align pattern | |||||||
| 22189 | 5' | -57.4 | NC_004927.1 | + | 50025 | 0.66 | 0.729175 |
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Target: 5'- uGGGGUUgguggUUCAaguaacUCACGAGCGGGGaaCGa -3' miRNA: 3'- -UCCCAG-----AAGU------GGUGCUCGCCUCagGC- -5' |
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| 22189 | 5' | -57.4 | NC_004927.1 | + | 44104 | 0.67 | 0.624855 |
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Target: 5'- --uGUgUUC-CCGCGAacGCGGAGUCCa -3' miRNA: 3'- uccCAgAAGuGGUGCU--CGCCUCAGGc -5' |
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| 22189 | 5' | -57.4 | NC_004927.1 | + | 13879 | 0.67 | 0.63541 |
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Target: 5'- cGGGUgUUCcgaCGCGAGCuGGuAGUCCc -3' miRNA: 3'- uCCCAgAAGug-GUGCUCG-CC-UCAGGc -5' |
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| 22189 | 5' | -57.4 | NC_004927.1 | + | 12233 | 0.69 | 0.531069 |
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Target: 5'- -cGGUUaUCGCCACGGuGCGGcuUCCGg -3' miRNA: 3'- ucCCAGaAGUGGUGCU-CGCCucAGGC- -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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