miRNA: 3'- cUCUC-GUGG----GUCUGCGCU---UGGCAacc -5'
miRNA: 3'- -CUCUCgUGGg--UC-----UGCGCU---UGGCAACC- -5'
miRNA: 3'- -CUCUCGU-------GGGUCUGcGCUUGGCaACC- -5'
miRNA: 3'- -CUCUCGUGGGUCUGCGCUUGGCAACC- -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 | |||||||
| 15341 | 5' | -55 | NC_003876.1 | + | 3828 | 0.66 | 0.129252 |
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Target: 5'- uGGAGaCACCggcaCGGGCGCGAgcgGCCGUa-- -3' miRNA: 3'- cUCUC-GUGG----GUCUGCGCU---UGGCAacc -5' |
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| 15341 | 5' | -55 | NC_003876.1 | + | 4456 | 0.68 | 0.092204 |
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Target: 5'- aGGGAGgACCacaAGaagcuGCGCGAauuGCUGUUGGg -3' miRNA: 3'- -CUCUCgUGGg--UC-----UGCGCU---UGGCAACC- -5' |
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| 15341 | 5' | -55 | NC_003876.1 | + | 3250 | 0.72 | 0.049327 |
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Target: 5'- cGAGAGCAauguccuUCUAGGC-CGAGCCGcUGGg -3' miRNA: 3'- -CUCUCGU-------GGGUCUGcGCUUGGCaACC- -5' |
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| 15341 | 5' | -55 | NC_003876.1 | + | 3249 | 1.09 | 0.00003 |
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Target: 5'- gGAGAGCACCCAGACGCGAACCGUUGGc -3' miRNA: 3'- -CUCUCGUGGGUCUGCGCUUGGCAACC- -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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