miRNA: 3'- -CGGcCUAGCGCcag-CGU-CUuAAGGCC- -5'
miRNA: 3'- -CG-GCCUAGCGCCa--GCGuCUuAAGGcc -5'
miRNA: 3'- cGGCCuaGcGCCAGCGu--CUuaAGGCC- -5'
miRNA: 3'- -CggCCu-----AGCGCCAGCGuCUUAa--GGCc -5'
miRNA: 3'- -CGGCCU--AGCGCCaGCGUCUuaa---GGCc -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 | |||||||
| 17178 | 3' | -54.9 | NC_004333.2 | + | 28695 | 0.67 | 0.688046 |
|
Target: 5'- uGCCaGAUCGCGagcaGCAcGAcUUCCGGc -3' miRNA: 3'- -CGGcCUAGCGCcag-CGU-CUuAAGGCC- -5' |
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| 17178 | 3' | -54.9 | NC_004333.2 | + | 28775 | 0.67 | 0.655429 |
|
Target: 5'- cGCgCGGGUCGCGGcggCGC-GAcUUCCc- -3' miRNA: 3'- -CG-GCCUAGCGCCa--GCGuCUuAAGGcc -5' |
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| 17178 | 3' | -54.9 | NC_004333.2 | + | 30464 | 0.66 | 0.720185 |
|
Target: 5'- uCCGGcgC-CGGUCGCuucGAcgUUCGGc -3' miRNA: 3'- cGGCCuaGcGCCAGCGu--CUuaAGGCC- -5' |
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| 17178 | 3' | -54.9 | NC_004333.2 | + | 40755 | 0.66 | 0.761775 |
|
Target: 5'- gGuuGGuguucuUUGCGGUCGC-GAGUgcgCCGa -3' miRNA: 3'- -CggCCu-----AGCGCCAGCGuCUUAa--GGCc -5' |
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| 17178 | 3' | -54.9 | NC_004333.2 | + | 45273 | 0.69 | 0.589882 |
|
Target: 5'- gGCCGGGcuUCGUGG-CGCGGAcagcugCCGc -3' miRNA: 3'- -CGGCCU--AGCGCCaGCGUCUuaa---GGCc -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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