miRNA: 3'- cCCGGAAgua-CG--UGuaGCGCCCUGUC- -5'
miRNA: 3'- -CCCGGaAGUA-CGUGUaGCGC-CCUGuc -5'
miRNA: 3'- -CCCGGAAGUa---CGUGuAGcGCCCUGUC- -5'
miRNA: 3'- -CCCG-GA-----------AGUACGUguaGCGCCCUGUC- -5'
miRNA: 3'- -CCCGGAAGUACGUGUAGCGCCCUGUC- -5'
Results 1 - 5 of 5 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 | |||||||
| 1130 | 5' | -55.6 | NC_000942.1 | + | 14077 | 0.66 | 0.5514 |
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Target: 5'- cGGUCUUauugGCgaGCcgCGUGGGGCAGu -3' miRNA: 3'- cCCGGAAgua-CG--UGuaGCGCCCUGUC- -5' |
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| 1130 | 5' | -55.6 | NC_000942.1 | + | 19488 | 0.69 | 0.349438 |
|
Target: 5'- gGGGCC-UCAUaGCGCAgCGUGuGGACu- -3' miRNA: 3'- -CCCGGaAGUA-CGUGUaGCGC-CCUGuc -5' |
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| 1130 | 5' | -55.6 | NC_000942.1 | + | 15871 | 0.7 | 0.299964 |
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Target: 5'- gGGGCUUUCAacagGCAU-UCaCGGGGCAGu -3' miRNA: 3'- -CCCGGAAGUa---CGUGuAGcGCCCUGUC- -5' |
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| 1130 | 5' | -55.6 | NC_000942.1 | + | 1912 | 0.74 | 0.174083 |
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Target: 5'- gGGGCgCUguuauaaagguUCAUGCAag-CGUGGGACAGc -3' miRNA: 3'- -CCCG-GA-----------AGUACGUguaGCGCCCUGUC- -5' |
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| 1130 | 5' | -55.6 | NC_000942.1 | + | 16443 | 1.11 | 0.000284 |
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Target: 5'- uGGGCCUUCAUGCACAUCGCGGGACAGg -3' miRNA: 3'- -CCCGGAAGUACGUGUAGCGCCCUGUC- -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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