miRNA: 3'- ugCGU--UAGCCGGAGCCuauuaGAugC- -5'
miRNA: 3'- -UGcGUUAGCCGGAGccuAUuAGAUGC- -5'
miRNA: 3'- -UGCGUUAGC--------------CGGAGCCUauuaGAUGC- -5'
miRNA: 3'- -UGCGuuAGCCGGAGCCUa----UUAGa---UGC- -5'
miRNA: 3'- -UGCGUUAGCCGGAGCCUAUUAGAUGC- -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 | |||||||
| 16656 | 5' | -50.5 | NC_004156.1 | + | 225371 | 0.66 | 0.998599 |
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Target: 5'- -aGCAgaGUUGGCCUCGGcagg-CUugGc -3' miRNA: 3'- ugCGU--UAGCCGGAGCCuauuaGAugC- -5' |
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| 16656 | 5' | -50.5 | NC_004156.1 | + | 106197 | 0.66 | 0.99832 |
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Target: 5'- uGC-CGAUCGGCCUCu--UGcUCUACGa -3' miRNA: 3'- -UGcGUUAGCCGGAGccuAUuAGAUGC- -5' |
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| 16656 | 5' | -50.5 | NC_004156.1 | + | 128791 | 0.68 | 0.994514 |
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Target: 5'- uAUGCAAUCGuccuugauggcauaGCCUCGGAcuc-CUACGc -3' miRNA: 3'- -UGCGUUAGC--------------CGGAGCCUauuaGAUGC- -5' |
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| 16656 | 5' | -50.5 | NC_004156.1 | + | 91765 | 0.71 | 0.971108 |
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Target: 5'- uACGC--UUGGCCUCGGAcucggAGUCggugGCGu -3' miRNA: 3'- -UGCGuuAGCCGGAGCCUa----UUAGa---UGC- -5' |
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| 16656 | 5' | -50.5 | NC_004156.1 | + | 201927 | 1.09 | 0.01608 |
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Target: 5'- uACGCAAUCGGCCUCGGAUAAUCUACGu -3' miRNA: 3'- -UGCGUUAGCCGGAGCCUAUUAGAUGC- -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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