miRNA: 3'- cGUGCa----CUACGGUCG----------CGUGuCCUCUU- -5'
miRNA: 3'- -CGUGCacuACGGUCGCG------UGUCCUcuu -5'
miRNA: 3'- -CGUGCACua--CGgUCGCGUGUCCucuu -5'
miRNA: 3'- -CGUGCACUACGGUCGCGUGUCCUCUU- -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 | |||||||
| 1077 | 5' | -55.8 | NC_000929.1 | + | 16692 | 0.66 | 0.517321 |
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Target: 5'- cCGCGaagugGAUGCCGGUacggaugaaaGCACcGGAGAGa -3' miRNA: 3'- cGUGCa----CUACGGUCG----------CGUGuCCUCUU- -5' |
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| 1077 | 5' | -55.8 | NC_000929.1 | + | 30178 | 0.67 | 0.474214 |
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Target: 5'- aGCACGc--UGCCAGCGUguaccgGCAGGAa-- -3' miRNA: 3'- -CGUGCacuACGGUCGCG------UGUCCUcuu -5' |
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| 1077 | 5' | -55.8 | NC_000929.1 | + | 20592 | 0.69 | 0.33129 |
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Target: 5'- cGUACGUGuauaGCgGGCGCACAGGu--- -3' miRNA: 3'- -CGUGCACua--CGgUCGCGUGUCCucuu -5' |
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| 1077 | 5' | -55.8 | NC_000929.1 | + | 14821 | 1.08 | 0.000488 |
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Target: 5'- gGCACGUGAUGCCAGCGCACAGGAGAAa -3' miRNA: 3'- -CGUGCACUACGGUCGCGUGUCCUCUU- -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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