miRNA: 3'- -CUGCGGUGgUCGU-----UGUGGGUgCGUcu -5'
miRNA: 3'- cugCGGUG------GUCGUUGUGGGUGcGUCU- -5'
miRNA: 3'- -CUGCGGUGGUC------------GUUG--UGGGUGCGucu -5'
miRNA: 3'- -CUGCGGUGGUCGUUGUGGGUGCGUCU- -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 | |||||||
| 3383 | 5' | -57.4 | NC_001564.1 | + | 3150 | 0.68 | 0.126388 |
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Target: 5'- cGAUGCCAUgGGCGaaugcACGCCCAgGUAa- -3' miRNA: 3'- -CUGCGGUGgUCGU-----UGUGGGUgCGUcu -5' |
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| 3383 | 5' | -57.4 | NC_001564.1 | + | 2860 | 0.69 | 0.104525 |
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Target: 5'- --gGCCAUucuuuaCGGCAACGCCCGC-CAGGu -3' miRNA: 3'- cugCGGUG------GUCGUUGUGGGUGcGUCU- -5' |
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| 3383 | 5' | -57.4 | NC_001564.1 | + | 4701 | 0.69 | 0.094975 |
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Target: 5'- aGGCGCUACCAGagugaggaacgaCAACucGCCCACGCc-- -3' miRNA: 3'- -CUGCGGUGGUC------------GUUG--UGGGUGCGucu -5' |
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| 3383 | 5' | -57.4 | NC_001564.1 | + | 3627 | 1.08 | 5.7e-05 |
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Target: 5'- gGACGCCACCAGCAACACCCACGCAGAu -3' miRNA: 3'- -CUGCGGUGGUCGUUGUGGGUGCGUCU- -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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