miRNA: 3'- cUGGUU-UCGGaCCAuCUGCCGGaaca -5'
miRNA: 3'- -CUGGU-------UUCGGA-----CCAUCuGCCGGAaca -5'
miRNA: 3'- cUG-GUUUCGGa----CCAUCUGCCGGAaca -5'
miRNA: 3'- -CUGGUUUCGGACCAUCUGCCGGAACA- -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 | |||||||
| 30808 | 5' | -54.3 | NC_006552.1 | + | 25627 | 0.66 | 0.755006 |
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Target: 5'- uACCAGuGGCCaGGUcGGCGGCCa--- -3' miRNA: 3'- cUGGUU-UCGGaCCAuCUGCCGGaaca -5' |
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| 30808 | 5' | -54.3 | NC_006552.1 | + | 61756 | 0.66 | 0.753965 |
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Target: 5'- cGACCAgcaugccAGGCCUguugcGGUGG-CGGCCUc-- -3' miRNA: 3'- -CUGGU-------UUCGGA-----CCAUCuGCCGGAaca -5' |
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| 30808 | 5' | -54.3 | NC_006552.1 | + | 50405 | 0.75 | 0.303531 |
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Target: 5'- aACgCAAAGCCaucugGGUGGGCGGCCUg-- -3' miRNA: 3'- cUG-GUUUCGGa----CCAUCUGCCGGAaca -5' |
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| 30808 | 5' | -54.3 | NC_006552.1 | + | 4451 | 1.06 | 0.001953 |
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Target: 5'- uGACCAAAGCCUGGUAGACGGCCUUGUc -3' miRNA: 3'- -CUGGUUUCGGACCAUCUGCCGGAACA- -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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