miRNA: 3'- -CCugCGGCgUUCCCAG-------AGAGCggCuG- -5'
miRNA: 3'- -CCUGcGGcGUUCCCAGAGaGCgGCUG- -5'
miRNA: 3'- cCUGCGGCG--UUCCCAGa-GAGCGgCUG- -5'
miRNA: 3'- -CCUGCGGCGUUCCCAGAGAGCGGCUG- -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 | |||||||
| 17997 | 5' | -58.9 | NC_004665.1 | + | 5215 | 0.66 | 0.430703 |
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Target: 5'- cGGugGCUG-AAGGGUCacggugaUCUCGuuGcCa -3' miRNA: 3'- -CCugCGGCgUUCCCAG-------AGAGCggCuG- -5' |
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| 17997 | 5' | -58.9 | NC_004665.1 | + | 24429 | 0.67 | 0.394336 |
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Target: 5'- uGGACaCCuCAAGGGUCUC-CG-UGACa -3' miRNA: 3'- -CCUGcGGcGUUCCCAGAGaGCgGCUG- -5' |
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| 17997 | 5' | -58.9 | NC_004665.1 | + | 25477 | 0.71 | 0.195347 |
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Target: 5'- cGGCGCUGCucAGGGGUCagCUUGCgGAUg -3' miRNA: 3'- cCUGCGGCG--UUCCCAGa-GAGCGgCUG- -5' |
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| 17997 | 5' | -58.9 | NC_004665.1 | + | 2221 | 1.11 | 0.000207 |
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Target: 5'- aGGACGCCGCAAGGGUCUCUCGCCGACu -3' miRNA: 3'- -CCUGCGGCGUUCCCAGAGAGCGGCUG- -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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