miRNA: 3'- -UCCGAGACCACAGCUAGGGAUACCAG- -5'
miRNA: 3'- ucCGAGACCACa-GCU--------AGGGAuaCCAG- -5'
miRNA: 3'- -UCCGa---GACCaCAGCuaGGgAUACCAG- -5'
miRNA: 3'- uCCGagACCACAGCUAG----GGa--UACCAG- -5'
miRNA: 3'- -UCCGAGACCa--CAGCuAGGga-----------UACCag -5'
Results 1 - 5 of 5 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand |
Start Position
|
R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 17965 | 3' | -55.2 | NC_004665.1 | + | 555 | 1.1 | 0.000466 |
|
Target: 5'- uAGGCUCUGGUGUCGAUCCCUAUGGUCa -3' miRNA: 3'- -UCCGAGACCACAGCUAGGGAUACCAG- -5' |
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| 17965 | 3' | -55.2 | NC_004665.1 | + | 4382 | 0.66 | 0.582878 |
|
Target: 5'- -aGCUCUGGUGacCGAcguggccuUCUCUggGGUCg -3' miRNA: 3'- ucCGAGACCACa-GCU--------AGGGAuaCCAG- -5' |
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| 17965 | 3' | -55.2 | NC_004665.1 | + | 5380 | 0.67 | 0.494525 |
|
Target: 5'- aAGGUacugCUGGaGUCGggCCaUGUGGUCa -3' miRNA: 3'- -UCCGa---GACCaCAGCuaGGgAUACCAG- -5' |
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| 17965 | 3' | -55.2 | NC_004665.1 | + | 14569 | 0.68 | 0.462939 |
|
Target: 5'- cGGUgaUGGUGUCGGUCgcaaCCacgAUGGUCa -3' miRNA: 3'- uCCGagACCACAGCUAG----GGa--UACCAG- -5' |
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| 17965 | 3' | -55.2 | NC_004665.1 | + | 22343 | 0.66 | 0.587406 |
|
Target: 5'- gAGGCUCUGGgugGUCGuUCCaagcaggcaccggGUGGa- -3' miRNA: 3'- -UCCGAGACCa--CAGCuAGGga-----------UACCag -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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