miRNA: 3'- ugCGCGCGG--ACCACgGGCgUCACaac -5'
miRNA: 3'- uGCG-CGCGGac-CACGGGCGUC----ACaaC- -5'
miRNA: 3'- -UGCGCGCGGAcCaCGGGCGU-------CACaac -5'
miRNA: 3'- -UGCGCGCGGACCACGGGCGUCACAAC- -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 | |||||||
| 3294 | 3' | -60.7 | NC_001545.1 | + | 6335 | 0.66 | 0.09594 |
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Target: 5'- -aGCGCGCCgaUGGUGgCCG-GGUGg-- -3' miRNA: 3'- ugCGCGCGG--ACCACgGGCgUCACaac -5' |
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| 3294 | 3' | -60.7 | NC_001545.1 | + | 6084 | 0.67 | 0.081888 |
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Target: 5'- cCGCgGUGCCgacGUGCCCGCAGaagcUGggGg -3' miRNA: 3'- uGCG-CGCGGac-CACGGGCGUC----ACaaC- -5' |
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| 3294 | 3' | -60.7 | NC_001545.1 | + | 5553 | 0.68 | 0.069591 |
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Target: 5'- cAUGCGCGCCUuGcGCCCGCAauuccuuGUGg-- -3' miRNA: 3'- -UGCGCGCGGAcCaCGGGCGU-------CACaac -5' |
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| 3294 | 3' | -60.7 | NC_001545.1 | + | 913 | 1.08 | 2.2e-05 |
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Target: 5'- cACGCGCGCCUGGUGCCCGCAGUGUUGg -3' miRNA: 3'- -UGCGCGCGGACCACGGGCGUCACAAC- -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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