miRNA: 3'- gCAGaGCAauuuUAcCACCCUCUGGG- -5'
miRNA: 3'- gCAG--AGCaau------------UUUACCACCC---UCUGGG- -5'
miRNA: 3'- -GCAgaGCAAUUUua---CCACCCUCUGGg -5'
miRNA: 3'- -GCAGAGCAAUUUUACCACCCUCUGGG- -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 |
| Predicted miRNA align pattern | |||||||
| 30267 | 5' | -48.7 | NC_006296.2 | + | 9150 | 0.68 | 0.610276 |
|
Target: 5'- gGUCcCGUc---AUuGUGGGAGGCCCu -3' miRNA: 3'- gCAGaGCAauuuUAcCACCCUCUGGG- -5' |
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| 30267 | 5' | -48.7 | NC_006296.2 | + | 5019 | 0.67 | 0.725379 |
|
Target: 5'- uGUCcuUCGguucugcgcugcucuGGGUGGUGGGcccGGGCCCu -3' miRNA: 3'- gCAG--AGCaau------------UUUACCACCC---UCUGGG- -5' |
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| 30267 | 5' | -48.7 | NC_006296.2 | + | 4602 | 0.67 | 0.685046 |
|
Target: 5'- cCGUg-UGUUGAGuucggGGUGGGGGGCUg -3' miRNA: 3'- -GCAgaGCAAUUUua---CCACCCUCUGGg -5' |
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| 30267 | 5' | -48.7 | NC_006296.2 | + | 266 | 1.15 | 0.000452 |
|
Target: 5'- cCGUCUCGUUAAAAUGGUGGGAGACCCa -3' miRNA: 3'- -GCAGAGCAAUUUUACCACCCUCUGGG- -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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