miRNA: 3'- gcGGAGUGGA-----GCCg---UCGCCAG----UCCAG- -5'
miRNA: 3'- gCGGAG-------UGGAGCCGUCGCCagucCAG- -5'
miRNA: 3'- gCGGAGUGGAg-----CCGUCGCCaGUCCag -5'
miRNA: 3'- -GCGGAGUGGAGCCGUCGCCAGUCCAG- -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 | |||||||
| 6181 | 3' | -60.7 | NC_001837.1 | + | 7673 | 0.67 | 0.09044 |
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Target: 5'- -cCCUCACCUcaucaCGGaugaGGUGGUCuucuGGGUCa -3' miRNA: 3'- gcGGAGUGGA-----GCCg---UCGCCAG----UCCAG- -5' |
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| 6181 | 3' | -60.7 | NC_001837.1 | + | 6099 | 0.7 | 0.050788 |
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Target: 5'- gGCCUCaccagggGCCUCGGUGGCGGgu--GUCg -3' miRNA: 3'- gCGGAG-------UGGAGCCGUCGCCagucCAG- -5' |
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| 6181 | 3' | -60.7 | NC_001837.1 | + | 9163 | 0.72 | 0.032391 |
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Target: 5'- aGCCUCGCUUggcacaGGCGGCGGgCGGGg- -3' miRNA: 3'- gCGGAGUGGAg-----CCGUCGCCaGUCCag -5' |
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| 6181 | 3' | -60.7 | NC_001837.1 | + | 6788 | 1.1 | 0.000017 |
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Target: 5'- cCGCCUCACCUCGGCAGCGGUCAGGUCg -3' miRNA: 3'- -GCGGAGUGGAGCCGUCGCCAGUCCAG- -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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