miRNA: 3'- cUCCGuCGUUa--AACGACGGgAuUUCU- -5'
miRNA: 3'- aACGUGCGGGCaAUGUuaugGGCACG- -5'
miRNA: 3'- cUCCGUCGUUaAACGACGGG-----AUUUCU- -5'
miRNA: 3'- -CUCCGUCGUUAAACGACGGGAUUUCU- -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 | |||||||
| 15259 | 3' | -49.8 | NC_003839.1 | + | 654 | 0.66 | 0.369397 |
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Target: 5'- aAGGCuGCGGcucUUGCUGCCgUuAAGGc -3' miRNA: 3'- cUCCGuCGUUa--AACGACGGgAuUUCU- -5' |
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| 15259 | 3' | -49.8 | NC_003839.1 | + | 2360 | 0.74 | 0.130315 |
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Target: 5'- cUGCACGCCCGaUGCG----UUGUGCa -3' miRNA: 3'- aACGUGCGGGCaAUGUuaugGGCACG- -5' |
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| 15259 | 3' | -49.8 | NC_003839.1 | + | 565 | 0.81 | 0.024974 |
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Target: 5'- aGGGCAGCAAaUUGCUGCCUcugugUAAGGGg -3' miRNA: 3'- cUCCGUCGUUaAACGACGGG-----AUUUCU- -5' |
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| 15259 | 3' | -49.8 | NC_003839.1 | + | 538 | 1.1 | 0.000119 |
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Target: 5'- aGAGGCAGCAAUUUGCUGCCCUAAAGAa -3' miRNA: 3'- -CUCCGUCGUUAAACGACGGGAUUUCU- -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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