miRNA: 3'- caGCGGCUCUUcCG---UACCC---UGCUCau -5'
miRNA: 3'- caGCGGCUCUU----------CCGUACC-CUG-CUCAu -5'
miRNA: 3'- caGCGGCUCUU--CCGUACCcUGCUcau -5'
miRNA: 3'- cagCGGCUCUUCCGUa----CCCUGCUcau -5'
miRNA: 3'- -CAGCGGCUCUUCCGUACCCUGCUCAU- -5'
Results 1 - 5 of 5 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 | |||||||
| 1446 | 5' | -56.5 | NC_001335.1 | + | 47640 | 0.66 | 0.599988 |
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Target: 5'- -cCGCCGAGAAaGCcucGUGGGuucACGAGg- -3' miRNA: 3'- caGCGGCUCUUcCG---UACCC---UGCUCau -5' |
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| 1446 | 5' | -56.5 | NC_001335.1 | + | 17722 | 0.67 | 0.556204 |
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Target: 5'- -cCGCCGAGGGauucggcaacGGCAUGGaGGCaGGGUu -3' miRNA: 3'- caGCGGCUCUU----------CCGUACC-CUG-CUCAu -5' |
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| 1446 | 5' | -56.5 | NC_001335.1 | + | 11431 | 0.68 | 0.502893 |
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Target: 5'- -aCGCCGAGGAacGGCGUGGuGCGGu-- -3' miRNA: 3'- caGCGGCUCUU--CCGUACCcUGCUcau -5' |
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| 1446 | 5' | -56.5 | NC_001335.1 | + | 723 | 0.7 | 0.367912 |
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Target: 5'- --gGUCGAGAAGGCGcucggGGGACGAc-- -3' miRNA: 3'- cagCGGCUCUUCCGUa----CCCUGCUcau -5' |
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| 1446 | 5' | -56.5 | NC_001335.1 | + | 7422 | 1.06 | 0.001053 |
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Target: 5'- gGUCGCCGAGAAGGCAUGGGACGAGUAc -3' miRNA: 3'- -CAGCGGCUCUUCCGUACCCUGCUCAU- -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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