miRNA: 3'- -UUGCCG----UUGG---------------GGGUGUUACCAGUUGu -5'
miRNA: 3'- -UUGCCGUugGGGg---------UGuUACCaGUUGU- -5'
miRNA: 3'- -UUGCCG----UUGGGGg----UGUUACCAGUUGU- -5'
miRNA: 3'- -UUGCCGUUGGGGGUGUUACCAGUUGU- -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 | |||||||
| 16557 | 3' | -53.6 | NC_004112.1 | + | 2750 | 0.67 | 0.636343 |
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Target: 5'- aAGCGGCugucGGCUuaucaguggaaauuuCCCAUGAUGGUCAAUg -3' miRNA: 3'- -UUGCCG----UUGG---------------GGGUGUUACCAGUUGu -5' |
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| 16557 | 3' | -53.6 | NC_004112.1 | + | 37811 | 0.68 | 0.585823 |
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Target: 5'- gGACGGCAugCCCaagucaccuaGCuAUGG-CAACAa -3' miRNA: 3'- -UUGCCGUugGGGg---------UGuUACCaGUUGU- -5' |
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| 16557 | 3' | -53.6 | NC_004112.1 | + | 1162 | 0.7 | 0.454234 |
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Target: 5'- cGAUGGCuaugAACCCCacguuGCGGUGGUUGACGa -3' miRNA: 3'- -UUGCCG----UUGGGGg----UGUUACCAGUUGU- -5' |
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| 16557 | 3' | -53.6 | NC_004112.1 | + | 18996 | 1.07 | 0.001315 |
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Target: 5'- cAACGGCAACCCCCACAAUGGUCAACAg -3' miRNA: 3'- -UUGCCGUUGGGGGUGUUACCAGUUGU- -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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