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miRNA: 3'- -UUCGGCa----UAUAGu------CGCGUGgCCCUUA- -5'
miRNA: 3'- uuCGG-CAUa-UAGUCG---------------CGUGGCCCUua -5'
miRNA: 3'- uucGGCaUAUAGUCGCGUg------GCCCUUA- -5'
miRNA: 3'- -UUCGGCAUAUAGUCGCGUGGCCCUUA- -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 | |||||||
| 1080 | 5' | -54.5 | NC_000929.1 | + | 15303 | 0.66 | 0.542859 |
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Target: 5'- uGAGCCGgucggAUAUUuaccgacGCGCAUgGGGAGUc -3' miRNA: 3'- -UUCGGCa----UAUAGu------CGCGUGgCCCUUA- -5' |
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| 1080 | 5' | -54.5 | NC_000929.1 | + | 18568 | 0.66 | 0.570298 |
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Target: 5'- -cGCCaGUGcgGUCAGCuuuuucaugccggugGCACCGGGGu- -3' miRNA: 3'- uuCGG-CAUa-UAGUCG---------------CGUGGCCCUua -5' |
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| 1080 | 5' | -54.5 | NC_000929.1 | + | 22314 | 0.68 | 0.476458 |
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Target: 5'- --cCCGgAUAUCAGCGCAaguaucgCGGGAAUg -3' miRNA: 3'- uucGGCaUAUAGUCGCGUg------GCCCUUA- -5' |
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| 1080 | 5' | -54.5 | NC_000929.1 | + | 17016 | 1.04 | 0.001175 |
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Target: 5'- gAAGCCGUAUAUCAGCGCACCGGGAAUa -3' miRNA: 3'- -UUCGGCAUAUAGUCGCGUGGCCCUUA- -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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