miRNA: 3'- -CGUCuu---CGUUuuGCU-UAGCAAGAGCc -5'
miRNA: 3'- -CGucuUCGUU----UUGCUUAGCAAGaGCc -5'
miRNA: 3'- -CGU------CUUCGUU----UUGCUUAGcAAGAGCc -5'
miRNA: 3'- -CGUCUUCgUUUUGCUUa--GCAa---GaGCc -5'
miRNA: 3'- -CGUC-----UUCGUUUUGC---UUAGCaa--GAGCc -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 | |||||||
| 12259 | 5' | -44.5 | NC_003309.1 | + | 4412 | 0.66 | 0.999524 |
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Target: 5'- aGCGGcucauGCGGggUGAgAUCGUUCUUGu -3' miRNA: 3'- -CGUCuu---CGUUuuGCU-UAGCAAGAGCc -5' |
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| 12259 | 5' | -44.5 | NC_003309.1 | + | 37467 | 0.66 | 0.999235 |
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Target: 5'- aGCu--GGCAAguccGACGAGUCGUUCaCGu -3' miRNA: 3'- -CGucuUCGUU----UUGCUUAGCAAGaGCc -5' |
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| 12259 | 5' | -44.5 | NC_003309.1 | + | 35165 | 0.66 | 0.999235 |
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Target: 5'- cGCAcggucuGGAGCAAagacAACGAGUUcUUCUCGu -3' miRNA: 3'- -CGU------CUUCGUU----UUGCUUAGcAAGAGCc -5' |
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| 12259 | 5' | -44.5 | NC_003309.1 | + | 37082 | 0.66 | 0.999235 |
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Target: 5'- aGCAGAAGgAGAACGAAcugCGUgcagC-CGa -3' miRNA: 3'- -CGUCUUCgUUUUGCUUa--GCAa---GaGCc -5' |
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| 12259 | 5' | -44.5 | NC_003309.1 | + | 46133 | 0.67 | 0.998524 |
|
Target: 5'- aGCAGcuucaAAGCAGAGCGcacGGUCGgcacCUCGa -3' miRNA: 3'- -CGUC-----UUCGUUUUGC---UUAGCaa--GAGCc -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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