miRNA: 3'- -CGAUAGUCGU--UGGGU-----------UGa---GGCgGCCG- -5'
miRNA: 3'- -CGAUAG----UCGu-UGGGuUGAGG-CGgCCG- -5'
miRNA: 3'- cgauaGUCGUUGgGUUGAGGCGGCCg -5'
miRNA: 3'- -CGAUAGUCGUUGGGUUGAGGCGGCCG- -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 | |||||||
| 13490 | 3' | -54.5 | NC_003417.1 | + | 10690 | 0.66 | 0.303272 |
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Target: 5'- cGCUGUCGGCGauAUCCAucgaaacggguAUguugCCGaCGGCg -3' miRNA: 3'- -CGAUAGUCGU--UGGGU-----------UGa---GGCgGCCG- -5' |
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| 13490 | 3' | -54.5 | NC_003417.1 | + | 8050 | 0.69 | 0.172965 |
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Target: 5'- cGCUGUCgccaGGCuuACCC-ACUCCuGUgGGCa -3' miRNA: 3'- -CGAUAG----UCGu-UGGGuUGAGG-CGgCCG- -5' |
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| 13490 | 3' | -54.5 | NC_003417.1 | + | 6075 | 0.69 | 0.172965 |
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Target: 5'- ----gUAGCAGCgCAGCUUCGCUGGa -3' miRNA: 3'- cgauaGUCGUUGgGUUGAGGCGGCCg -5' |
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| 13490 | 3' | -54.5 | NC_003417.1 | + | 11094 | 1.15 | 4.4e-05 |
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Target: 5'- aGCUAUCAGCAACCCAACUCCGCCGGCa -3' miRNA: 3'- -CGAUAGUCGUUGGGUUGAGGCGGCCG- -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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