miRNA: 3'- -GUCaAGACCG--UACUUAGC---------------GUUGCGUc -5'
miRNA: 3'- gUCAAG----ACCGuACUUAGCGuuGC-GUC- -5'
miRNA: 3'- -GUCAAGa--CCgu-ACUUAGCGUUGCGUc -5'
miRNA: 3'- -GUCaAGACCGuaCU--UAGCGUuGCGUC- -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 | |||||||
| 20918 | 3' | -49.9 | NC_004689.1 | + | 28645 | 0.67 | 0.926371 |
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Target: 5'- cCGG-UCUGGCcgGUGAGUCGagcgaagccguuccaCAGCGCAu -3' miRNA: 3'- -GUCaAGACCG--UACUUAGC---------------GUUGCGUc -5' |
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| 20918 | 3' | -49.9 | NC_004689.1 | + | 23736 | 0.69 | 0.874589 |
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Target: 5'- aAGUUCuuugUGGCcUGAAUCGCuuCGaCAGu -3' miRNA: 3'- gUCAAG----ACCGuACUUAGCGuuGC-GUC- -5' |
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| 20918 | 3' | -49.9 | NC_004689.1 | + | 39227 | 0.72 | 0.696197 |
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Target: 5'- uCAGUUCaccGGacuUGAGUUGCAGCGCAa -3' miRNA: 3'- -GUCAAGa--CCgu-ACUUAGCGUUGCGUc -5' |
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| 20918 | 3' | -49.9 | NC_004689.1 | + | 45039 | 0.75 | 0.527615 |
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Target: 5'- aCGG-UCUGGCggGAuuGUCGCAuCGCAGa -3' miRNA: 3'- -GUCaAGACCGuaCU--UAGCGUuGCGUC- -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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