miRNA: 3'- agaCCCCa----GCC-GCAGU------UCCGGUGAGU- -5'
miRNA: 3'- -AGACCCCAGC--CGcAGuUCCGGUGa-GU- -5'
miRNA: 3'- aGACCCCA-----GCCgCaGUUc-CGGUGAGU- -5'
miRNA: 3'- -AGACCCCAGCCGCAGUUCCGGUGAGU- -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 | |||||||
| 18003 | 3' | -58.8 | NC_004665.1 | + | 34247 | 0.66 | 0.388769 |
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Target: 5'- --aGGGGaacgaCGGuCGUCAucacgaAGGUCGCUCAg -3' miRNA: 3'- agaCCCCa----GCC-GCAGU------UCCGGUGAGU- -5' |
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| 18003 | 3' | -58.8 | NC_004665.1 | + | 18833 | 0.67 | 0.362187 |
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Target: 5'- cUCUGGGGUCGcuGC-UC-AGGCUACcgCAa -3' miRNA: 3'- -AGACCCCAGC--CGcAGuUCCGGUGa-GU- -5' |
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| 18003 | 3' | -58.8 | NC_004665.1 | + | 18894 | 0.68 | 0.312914 |
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Target: 5'- gCUGGGGUucaacCGGgGcCAAucGCCACUCAg -3' miRNA: 3'- aGACCCCA-----GCCgCaGUUc-CGGUGAGU- -5' |
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| 18003 | 3' | -58.8 | NC_004665.1 | + | 4406 | 1.09 | 0.000279 |
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Target: 5'- cUCUGGGGUCGGCGUCAAGGCCACUCAg -3' miRNA: 3'- -AGACCCCAGCCGCAGUUCCGGUGAGU- -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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