miRNA: 3'- -UCAGGGag-----CUCUG-----------GGCAG------AGCAUCCU- -5'
miRNA: 3'- uCAGGGAGCUCUGG--GCa--Gag-CAUCCu -5'
miRNA: 3'- uCAGGGa--------GCUCUGGGC------AGAgCAUCCU- -5'
miRNA: 3'- -UCAGGGAGCUCUGGGCAGAGCAUCCU- -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 | |||||||
| 13334 | 3' | -56.9 | NC_003409.1 | + | 76192 | 0.66 | 0.886681 |
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Target: 5'- uGGUCCCguuuaggGAGACggccucuagggCCGUCauauucUCGUAGGAa -3' miRNA: 3'- -UCAGGGag-----CUCUG-----------GGCAG------AGCAUCCU- -5' |
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| 13334 | 3' | -56.9 | NC_003409.1 | + | 131501 | 0.66 | 0.857758 |
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Target: 5'- uGUCCCUCGGGGCCaaCGgugCccaGUGGGu -3' miRNA: 3'- uCAGGGAGCUCUGG--GCa--Gag-CAUCCu -5' |
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| 13334 | 3' | -56.9 | NC_003409.1 | + | 100015 | 0.7 | 0.674942 |
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Target: 5'- uGUCCCgcagacaccUGAGACCCGcgucgcUCUgGUGGGAc -3' miRNA: 3'- uCAGGGa--------GCUCUGGGC------AGAgCAUCCU- -5' |
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| 13334 | 3' | -56.9 | NC_003409.1 | + | 108462 | 1.08 | 0.002609 |
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Target: 5'- cAGUCCCUCGAGACCCGUCUCGUAGGAu -3' miRNA: 3'- -UCAGGGAGCUCUGGGCAGAGCAUCCU- -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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