miRNA: 3'- -CGgUAGUCGU-CUGACA---------GCCAUUA----GAG- -5'
miRNA: 3'- cGGuAgUCGUCUGACAG------CCAUUAGAG- -5'
miRNA: 3'- -CGGuaGUCGUCUgaCA-GCCAUUA-GAG- -5'
miRNA: 3'- -CGGUAGUCGUCUGACAGCCAUUAGAG- -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 | |||||||
| 8467 | 5' | -50.4 | NC_002167.1 | + | 7214 | 0.67 | 0.818418 |
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Target: 5'- uGCgAUCAGCAuGGCUGUaguagcugcCGGUGGUaagcCUCc -3' miRNA: 3'- -CGgUAGUCGU-CUGACA---------GCCAUUA----GAG- -5' |
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| 8467 | 5' | -50.4 | NC_002167.1 | + | 28455 | 0.69 | 0.722099 |
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Target: 5'- aCCcUgAGCAGGCUGUUgagccaGGUGAUUUCu -3' miRNA: 3'- cGGuAgUCGUCUGACAG------CCAUUAGAG- -5' |
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| 8467 | 5' | -50.4 | NC_002167.1 | + | 23122 | 0.7 | 0.664392 |
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Target: 5'- cGCUggUAGCGGAgaGUgCGGUAAUgCUCg -3' miRNA: 3'- -CGGuaGUCGUCUgaCA-GCCAUUA-GAG- -5' |
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| 8467 | 5' | -50.4 | NC_002167.1 | + | 29999 | 1.14 | 0.000951 |
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Target: 5'- aGCCAUCAGCAGACUGUCGGUAAUCUCg -3' miRNA: 3'- -CGGUAGUCGUCUGACAGCCAUUAGAG- -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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