miRNA: 3'- cuaCGCGGCG-------GCC-AGCuGCCGUUCUU- -5'
miRNA: 3'- cuacgCGGCGGCC--AGCUGCCGuucuu -5'
miRNA: 3'- cUACGCGgCG---------------GCC----------AGCUGCCGUUCUU- -5'
miRNA: 3'- cuACGCGGCGGCCa------GCuGCCGUUCuu -5'
Results 21 - 24 of 24 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 | |||||||
| 12484 | 3' | -59.3 | NC_003324.1 | + | 49296 | 0.67 | 0.432704 |
|
Target: 5'- --gGCGUCGCaggcguuCGGaUCGuCGGCAGGAAg -3' miRNA: 3'- cuaCGCGGCG-------GCC-AGCuGCCGUUCUU- -5' |
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| 12484 | 3' | -59.3 | NC_003324.1 | + | 2507 | 0.66 | 0.452805 |
|
Target: 5'- ----aGCCGCCGGcgUCGGCGGCu---- -3' miRNA: 3'- cuacgCGGCGGCC--AGCUGCCGuucuu -5' |
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| 12484 | 3' | -59.3 | NC_003324.1 | + | 47689 | 0.66 | 0.496492 |
|
Target: 5'- cAUGCGCgGCgugguaaagcucggaCGGaacuuccggcUCGACGGCGAGGGu -3' miRNA: 3'- cUACGCGgCG---------------GCC----------AGCUGCCGUUCUU- -5' |
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| 12484 | 3' | -59.3 | NC_003324.1 | + | 14665 | 0.74 | 0.160997 |
|
Target: 5'- -cUGCGCCGCCGGccgcuugCGcCGGCAGGc- -3' miRNA: 3'- cuACGCGGCGGCCa------GCuGCCGUUCuu -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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