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miRNA: 3'- ccaaGCCUGCGUCGUC-ACUCAca-CCC- -5'
miRNA: 3'- -CCA------AGCcUGCGU-CGU---CACUCaCACCC- -5'
miRNA: 3'- -CCA--------AGCCug---CGUC-GUCACUCaCACCC- -5'
miRNA: 3'- -CCAAGCCUGCGUCGUCACUCACACCC- -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 | |||||||
| 23196 | 5' | -54.4 | NC_005259.1 | + | 23285 | 0.66 | 0.841634 |
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Target: 5'- ---cCGGGCGCGGUGGuUGGGUaucGGGg -3' miRNA: 3'- ccaaGCCUGCGUCGUC-ACUCAca-CCC- -5' |
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| 23196 | 5' | -54.4 | NC_005259.1 | + | 12803 | 0.66 | 0.850087 |
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Target: 5'- cGGUacgcugUCGcGCGCAcGCGcgcGUGAGgGUGGGg -3' miRNA: 3'- -CCA------AGCcUGCGU-CGU---CACUCaCACCC- -5' |
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| 23196 | 5' | -54.4 | NC_005259.1 | + | 68818 | 0.7 | 0.63039 |
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Target: 5'- cGGUacaugcucUCGGucaaaGCAGuCGGUGAG-GUGGGc -3' miRNA: 3'- -CCA--------AGCCug---CGUC-GUCACUCaCACCC- -5' |
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| 23196 | 5' | -54.4 | NC_005259.1 | + | 62437 | 1.12 | 0.001135 |
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Target: 5'- aGGUUCGGACGCAGCAGUGAGUGUGGGc -3' miRNA: 3'- -CCAAGCCUGCGUCGUCACUCACACCC- -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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