miRNA: 3'- -GGGGUCaGUGGUUCuUGUaGUUGaug -5'
miRNA: 3'- gggGUCAGUGGUUCUUGUaGU-----UGAUG- -5'
miRNA: 3'- gGGGUCag------UGGUUCUUGUa---GUUGAUG- -5'
miRNA: 3'- -GGGGUCAGUGGUUCUUGUAGUUGAUG- -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 | |||||||
| 2494 | 5' | -48.3 | NC_001451.1 | + | 26900 | 0.66 | 0.899849 |
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Target: 5'- uCUCCAG-CGCCAAG-ACAaCAGCg-- -3' miRNA: 3'- -GGGGUCaGUGGUUCuUGUaGUUGaug -5' |
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| 2494 | 5' | -48.3 | NC_001451.1 | + | 11301 | 0.67 | 0.866819 |
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Target: 5'- --aCAGUCGCUAGGGGCA-CAacaccACUACu -3' miRNA: 3'- gggGUCAGUGGUUCUUGUaGU-----UGAUG- -5' |
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| 2494 | 5' | -48.3 | NC_001451.1 | + | 7698 | 0.73 | 0.503369 |
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Target: 5'- aCCCAGgacacaaaACCAGGAACAccugUAGCUACu -3' miRNA: 3'- gGGGUCag------UGGUUCUUGUa---GUUGAUG- -5' |
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| 2494 | 5' | -48.3 | NC_001451.1 | + | 3216 | 1.12 | 0.001493 |
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Target: 5'- uCCCCAGUCACCAAGAACAUCAACUACc -3' miRNA: 3'- -GGGGUCAGUGGUUCUUGUAGUUGAUG- -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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