miRNA: 3'- agUGACGGCgGGCCcaUUAGCACUUG- -5'
miRNA: 3'- -AGUGa---CGGCGGGC-----------CcaUUAGCACUUG- -5'
miRNA: 3'- aGUGACGGCGGGCC-CAUuaGCa-CUUg -5'
miRNA: 3'- -AGUGACGGCGGGCCCAUUAGCACUUG- -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 | |||||||
| 12172 | 5' | -54.8 | NC_003309.1 | + | 30740 | 0.66 | 0.738652 |
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Target: 5'- -uGCUGCCGaUCGGc-AAUCGUGAAUg -3' miRNA: 3'- agUGACGGCgGGCCcaUUAGCACUUG- -5' |
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| 12172 | 5' | -54.8 | NC_003309.1 | + | 32187 | 0.67 | 0.662648 |
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Target: 5'- gUCGCcgacGCCGCCCGcacccaagagaGcaAAUCGUGAGCg -3' miRNA: 3'- -AGUGa---CGGCGGGC-----------CcaUUAGCACUUG- -5' |
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| 12172 | 5' | -54.8 | NC_003309.1 | + | 44174 | 0.71 | 0.428702 |
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Target: 5'- gCGCUGCCGCUCGGcGUAcgCGacGAGu -3' miRNA: 3'- aGUGACGGCGGGCC-CAUuaGCa-CUUg -5' |
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| 12172 | 5' | -54.8 | NC_003309.1 | + | 43073 | 1.11 | 0.000807 |
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Target: 5'- cUCACUGCCGCCCGGGUAAUCGUGAACa -3' miRNA: 3'- -AGUGACGGCGGGCCCAUUAGCACUUG- -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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