miRNA: 3'- -CGCg---GCCUGCUacaUAACUAGCGGGu -5'
miRNA: 3'- -CGCGG--CCUGCUa---------CAUAACU--AGCGgGU- -5'
miRNA: 3'- cGCG-GCCUGCUACauaACU-AGCGGGU- -5'
miRNA: 3'- -CGCGGCCUGCUACAUAACUAGCGGGU- -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 | |||||||
| 32249 | 3' | -53.5 | NC_007022.1 | + | 150651 | 0.66 | 0.980584 |
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Target: 5'- cGUGgucaCGGAUGAacgGUUGAUCGCCUu -3' miRNA: 3'- -CGCg---GCCUGCUacaUAACUAGCGGGu -5' |
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| 32249 | 3' | -53.5 | NC_007022.1 | + | 109718 | 0.66 | 0.980584 |
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Target: 5'- uGCGCCauGGAUGAgccgaauaacGUGUUGAugUCGCgCAa -3' miRNA: 3'- -CGCGG--CCUGCUa---------CAUAACU--AGCGgGU- -5' |
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| 32249 | 3' | -53.5 | NC_007022.1 | + | 88159 | 0.7 | 0.88164 |
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Target: 5'- uCGCgCGGGCGAUGg--UGAuUUGCCUAu -3' miRNA: 3'- cGCG-GCCUGCUACauaACU-AGCGGGU- -5' |
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| 32249 | 3' | -53.5 | NC_007022.1 | + | 87597 | 1.11 | 0.004607 |
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Target: 5'- aGCGCCGGACGAUGUAUUGAUCGCCCAu -3' miRNA: 3'- -CGCGGCCUGCUACAUAACUAGCGGGU- -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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