miRNA: 3'- aacuUCACGCAUCU-----------GCGGCGGGaGCc -5'
miRNA: 3'- aaCUUCACg---CAUCU--GCGGcGGGAGCC- -5'
miRNA: 3'- -AACuUCACGcauc--UGCG-GCGGGAGCC- -5'
miRNA: 3'- aACUUCa--CGCauCUGCGGCGggaGCC- -5'
miRNA: 3'- -AACUUCACGCAUCUGCGGCGGGAGCC- -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 | |||||||
| 3313 | 3' | -56.7 | NC_001545.1 | + | 7665 | 0.67 | 0.160891 |
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Target: 5'- ---uGGUGUGUGGAgcacgaccgacCGCCGCCCgCGa -3' miRNA: 3'- aacuUCACGCAUCU-----------GCGGCGGGaGCc -5' |
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| 3313 | 3' | -56.7 | NC_001545.1 | + | 3863 | 0.68 | 0.133396 |
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Target: 5'- -cGAAGUGgccgGUGGGguUGCCcCCCUCGGg -3' miRNA: 3'- aaCUUCACg---CAUCU--GCGGcGGGAGCC- -5' |
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| 3313 | 3' | -56.7 | NC_001545.1 | + | 5987 | 0.69 | 0.110288 |
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Target: 5'- cUUG-AGUGCcgcgcuGCGCgCGCCCUCGGg -3' miRNA: 3'- -AACuUCACGcauc--UGCG-GCGGGAGCC- -5' |
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| 3313 | 3' | -56.7 | NC_001545.1 | + | 8211 | 0.69 | 0.106821 |
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Target: 5'- gUGAGGgcgGCGgcGGCGCCGCgg-CGGc -3' miRNA: 3'- aACUUCa--CGCauCUGCGGCGggaGCC- -5' |
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| 3313 | 3' | -56.7 | NC_001545.1 | + | 5406 | 1.07 | 8.1e-05 |
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Target: 5'- cUUGAAGUGCGUAGACGCCGCCCUCGGc -3' miRNA: 3'- -AACUUCACGCAUCUGCGGCGGGAGCC- -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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