miRNA: 3'- -GGGgCGGCaCC------AUGAGA----AGACUGGGU- -5'
miRNA: 3'- -GGGGCGGCa-----CCAUGagAAGAcuGGGU- -5'
miRNA: 3'- -GGGGCG-------GCACCau-GAGAAG---------ACUGGGU- -5'
miRNA: 3'- -GGGGCGGCACCAUGAGAAGACUGGGU- -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 | |||||||
| 22272 | 5' | -57 | NC_005045.1 | + | 11448 | 0.66 | 0.562281 |
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Target: 5'- gCCCgGCUGcGGaagcgaUGCUCUaccuUCUGGCCUAc -3' miRNA: 3'- -GGGgCGGCaCC------AUGAGA----AGACUGGGU- -5' |
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| 22272 | 5' | -57 | NC_005045.1 | + | 23430 | 0.67 | 0.530119 |
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Target: 5'- gCUCCGCCGgcugcgGGUGCagUUCUu-CCCGa -3' miRNA: 3'- -GGGGCGGCa-----CCAUGagAAGAcuGGGU- -5' |
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| 22272 | 5' | -57 | NC_005045.1 | + | 25172 | 0.67 | 0.508009 |
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Target: 5'- aCCCCGCacuucggUGUGGgguUUCUUCaaagccuaaUGACCCGc -3' miRNA: 3'- -GGGGCG-------GCACCau-GAGAAG---------ACUGGGU- -5' |
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| 22272 | 5' | -57 | NC_005045.1 | + | 28784 | 1.1 | 0.00044 |
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Target: 5'- gCCCCGCCGUGGUACUCUUCUGACCCAg -3' miRNA: 3'- -GGGGCGGCACCAUGAGAAGACUGGGU- -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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