miRNA: 3'- aUUUUCu--CGAAGAGCUa-----AGCCGAcuu -5'
miRNA: 3'- auuuuCUCGAa---GAGCUaaGCCGACUU- -5'
miRNA: 3'- aUUUUCuCGAAG-AGCUa-----AGCCGACUu -5'
miRNA: 3'- aUUUUCUCGaa-GAGCUaaGCCGACUu -5'
miRNA: 3'- -AUUUUCUCGAAGAGCUAAGCCGACUU- -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 | |||||||
| 12355 | 3' | -47.9 | NC_003324.1 | + | 1387 | 0.66 | 0.964207 |
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Target: 5'- cGGAGGcguGCUUCUCGAcccaugUCGGCUu-- -3' miRNA: 3'- aUUUUCu--CGAAGAGCUa-----AGCCGAcuu -5' |
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| 12355 | 3' | -47.9 | NC_003324.1 | + | 14758 | 0.67 | 0.941207 |
|
Target: 5'- ----uGGGCUgcagCUCGA--CGGCUGGAa -3' miRNA: 3'- auuuuCUCGAa---GAGCUaaGCCGACUU- -5' |
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| 12355 | 3' | -47.9 | NC_003324.1 | + | 40276 | 0.68 | 0.923634 |
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Target: 5'- gAGAAGcGCUUCgUCGGcaucgcUCGGCUGAu -3' miRNA: 3'- aUUUUCuCGAAG-AGCUa-----AGCCGACUu -5' |
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| 12355 | 3' | -47.9 | NC_003324.1 | + | 39733 | 0.69 | 0.895721 |
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Target: 5'- gAAGAGGGCgcgCUCGG--UGGCUGGc -3' miRNA: 3'- aUUUUCUCGaa-GAGCUaaGCCGACUu -5' |
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| 12355 | 3' | -47.9 | NC_003324.1 | + | 25434 | 1.05 | 0.008738 |
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Target: 5'- cUAAAAGAGCUUCUCGAUUCGGCUGAAu -3' miRNA: 3'- -AUUUUCUCGAAGAGCUAAGCCGACUU- -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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