miRNA: 3'- -UGCCCG--CCCCa---CCAaacUUGUGUGGC- -5'
miRNA: 3'- -UGCCCGCC-----CC--ACCAAAC--UUGUGUGGc -5'
miRNA: 3'- -UGCCCGCCCCACCAAACUUGUGUGGC- -5'
Results 1 - 3 of 3 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. |
strand
|
Start Position | R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 28196 | 3' | -56.6 | NC_005891.1 | + | 39482 | 0.66 | 0.558009 |
|
Target: 5'- gAUGGGCaaGGGGcacaGGU---AACGCGCCGa -3' miRNA: 3'- -UGCCCG--CCCCa---CCAaacUUGUGUGGC- -5' |
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| 28196 | 3' | -56.6 | NC_005891.1 | + | 25571 | 0.67 | 0.514918 |
|
Target: 5'- uACGGGUGGuugauGGacUGGUUUGcuGACGCACUc -3' miRNA: 3'- -UGCCCGCC-----CC--ACCAAAC--UUGUGUGGc -5' |
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| 28196 | 3' | -56.6 | NC_005891.1 | + | 8509 | 1.08 | 0.000629 |
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Target: 5'- aACGGGCGGGGUGGUUUGAACACACCGu -3' miRNA: 3'- -UGCCCGCCCCACCAAACUUGUGUGGC- -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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