miRNA: 3'- uGGAGAGuUUGAC-----GGGCUGCUGaaau -5'
miRNA: 3'- uGGaGAGUUUGACGG--GCUGCUGaaau -5'
miRNA: 3'- -UGGAGagUUUGACGGgC--UGCUGAAau -5'
miRNA: 3'- -UGGAGAGUUUGACGGGCUGCUGAAAU- -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 | |||||||
| 905 | 3' | -51.2 | NC_000899.1 | + | 18926 | 0.66 | 0.838388 |
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Target: 5'- cCCUUUC-AGCUGuuuucCCCGGCGACg--- -3' miRNA: 3'- uGGAGAGuUUGAC-----GGGCUGCUGaaau -5' |
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| 905 | 3' | -51.2 | NC_000899.1 | + | 7515 | 0.69 | 0.678467 |
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Target: 5'- cCCcCUCAGGCUGCUcgCGGCGGCg--- -3' miRNA: 3'- uGGaGAGUUUGACGG--GCUGCUGaaau -5' |
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| 905 | 3' | -51.2 | NC_000899.1 | + | 936 | 0.7 | 0.608872 |
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Target: 5'- uACCUCggGGGCUGCCgGuuACGACUUg- -3' miRNA: 3'- -UGGAGagUUUGACGGgC--UGCUGAAau -5' |
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| 905 | 3' | -51.2 | NC_000899.1 | + | 10267 | 1.07 | 0.002392 |
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Target: 5'- aACCUCUCAAACUGCCCGACGACUUUAa -3' miRNA: 3'- -UGGAGAGUUUGACGGGCUGCUGAAAU- -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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