miRNA: 3'- caCGUCcAGUGCCAcgCGCGCGAGCu -5'
miRNA: 3'- -CACGUcCAGU----GCCac-GCGCGCGAGCU- -5'
miRNA: 3'- caCGUc--CAGUGcCACGCGCGCGAGCU- -5'
miRNA: 3'- caCGuCCAGUGCCA-C-GCGCGCGAGcu -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 | |||||||
| 12210 | 3' | -59.9 | NC_003309.1 | + | 33990 | 0.66 | 0.433309 |
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Target: 5'- -cGCAGuUCGCGGUaaGCGUGUUCGc -3' miRNA: 3'- caCGUCcAGUGCCAcgCGCGCGAGCu -5' |
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| 12210 | 3' | -59.9 | NC_003309.1 | + | 22012 | 0.68 | 0.337607 |
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Target: 5'- cGUGCAcGUCAggacCGGcucCGCGUGCUCGAu -3' miRNA: 3'- -CACGUcCAGU----GCCac-GCGCGCGAGCU- -5' |
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| 12210 | 3' | -59.9 | NC_003309.1 | + | 17810 | 0.68 | 0.329707 |
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Target: 5'- -gGCGaucGUCGCcGUGUGCGCGUUCGGc -3' miRNA: 3'- caCGUc--CAGUGcCACGCGCGCGAGCU- -5' |
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| 12210 | 3' | -59.9 | NC_003309.1 | + | 10894 | 0.7 | 0.258237 |
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Target: 5'- -cGC-GGUCGCGGUcGcCGCGCGUUCc- -3' miRNA: 3'- caCGuCCAGUGCCA-C-GCGCGCGAGcu -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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