miRNA: 3'- cUCGGCCG---------------UCUGG---UCGUCCGGcUUGA- -5'
miRNA: 3'- cuCGGC-CGUCUGGucguCCGGCUUGA- -5'
miRNA: 3'- cUCGGCCG---UCUGGUCG--UC-CG-GCUUGa -5'
miRNA: 3'- cUCGGC-CGu----CUGGUC---GUCCGGC-UUGa -5'
miRNA: 3'- cUCGGCCGUCUGgucGUCCg---GCUUGa -5'
Results 21 - 25 of 25 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 | |||||||
| 30768 | 3' | -60.3 | NC_006552.1 | + | 60356 | 0.7 | 0.280194 |
|
Target: 5'- uGGCCGGCgaagggccagucgcuAGACCacaAGCGGGCC-AACUc -3' miRNA: 3'- cUCGGCCG---------------UCUGG---UCGUCCGGcUUGA- -5' |
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| 30768 | 3' | -60.3 | NC_006552.1 | + | 21433 | 0.69 | 0.284336 |
|
Target: 5'- -uGCCGcGCAGGCCcc--GGCCGAACUu -3' miRNA: 3'- cuCGGC-CGUCUGGucguCCGGCUUGA- -5' |
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| 30768 | 3' | -60.3 | NC_006552.1 | + | 32705 | 0.69 | 0.29849 |
|
Target: 5'- cGGCCGGCgcgGGGCCGGUggAGcGCuCGAACa -3' miRNA: 3'- cUCGGCCG---UCUGGUCG--UC-CG-GCUUGa -5' |
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| 30768 | 3' | -60.3 | NC_006552.1 | + | 32530 | 0.69 | 0.313184 |
|
Target: 5'- aAGCCGuGCugcuuGACCAGguuCAGGCCGuAGCg -3' miRNA: 3'- cUCGGC-CGu----CUGGUC---GUCCGGC-UUGa -5' |
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| 30768 | 3' | -60.3 | NC_006552.1 | + | 33703 | 0.66 | 0.488785 |
|
Target: 5'- aAGCCGGCGGGCaa-CGGGaacuCGAACg -3' miRNA: 3'- cUCGGCCGUCUGgucGUCCg---GCUUGa -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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