miRNA: 3'- -CGGGGGgGACau-CGUGGG-------------CCGG-GGCG- -5'
miRNA: 3'- cgGGGGgGaCA-----------UCGUGGgCCGGGGCG- -5'
miRNA: 3'- -CGGGGGGg--ACau--CGuGGGCCG-----GGGCG- -5'
miRNA: 3'- -CGGGGGGGACAUCGUGGGCCGGGGCG- -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 | |||||||
| 7605 | 5' | -65.7 | NC_001963.1 | + | 2144 | 0.67 | 0.02133 |
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Target: 5'- gGCCUCCgCUGcacGCGCCCgucuuuacggccgGGCCaCCGUa -3' miRNA: 3'- -CGGGGGgGACau-CGUGGG-------------CCGG-GGCG- -5' |
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| 7605 | 5' | -65.7 | NC_001963.1 | + | 2347 | 0.67 | 0.019377 |
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Target: 5'- -aCCCCgCaGUgccggugccacAGCACCaGGCCCUGCg -3' miRNA: 3'- cgGGGGgGaCA-----------UCGUGGgCCGGGGCG- -5' |
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| 7605 | 5' | -65.7 | NC_001963.1 | + | 2384 | 0.67 | 0.018746 |
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Target: 5'- cGCCCCUCagaUGccacGC-CCCGGCccgaaCCCGCa -3' miRNA: 3'- -CGGGGGGg--ACau--CGuGGGCCG-----GGGCG- -5' |
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| 7605 | 5' | -65.7 | NC_001963.1 | + | 2525 | 1.1 | 0.000001 |
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Target: 5'- uGCCCCCCCUGUAGCACCCGGCCCCGCc -3' miRNA: 3'- -CGGGGGGGACAUCGUGGGCCGGGGCG- -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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