miRNA: 3'- ucauCCaACUCC----CGCGGAUCCACagu -5'
miRNA: 3'- uCAuCCaa--CUCCCGCGGAUCCAcagu -5'
miRNA: 3'- -UCAUCCAa-CUCCCGCGGa----------UCCACAGu -5'
miRNA: 3'- -UCAUCCAACUCCCGCGGAUCCACAGU- -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 | |||||||
| 8130 | 5' | -55.6 | NC_001978.2 | + | 9099 | 0.66 | 0.591791 |
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Target: 5'- ---cGGcUGAGGcuaaGCGCCUGGGUGa-- -3' miRNA: 3'- ucauCCaACUCC----CGCGGAUCCACagu -5' |
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| 8130 | 5' | -55.6 | NC_001978.2 | + | 107 | 0.68 | 0.451471 |
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Target: 5'- cGUuGGccugGGGGGCGCCUGGGUc--- -3' miRNA: 3'- uCAuCCaa--CUCCCGCGGAUCCAcagu -5' |
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| 8130 | 5' | -55.6 | NC_001978.2 | + | 41001 | 0.73 | 0.236438 |
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Target: 5'- gAGUAGGUagGGGGGUGUCgacggauagggGGGUGUCc -3' miRNA: 3'- -UCAUCCAa-CUCCCGCGGa----------UCCACAGu -5' |
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| 8130 | 5' | -55.6 | NC_001978.2 | + | 27561 | 1.09 | 0.000572 |
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Target: 5'- gAGUAGGUUGAGGGCGCCUAGGUGUCAg -3' miRNA: 3'- -UCAUCCAACUCCCGCGGAUCCACAGU- -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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