miRNA: 3'- uaGGUGGCGCGgUCGGAGaaG--------------GCCaa -5'
miRNA: 3'- uaGG-UGGCGCGG--UCGGAGAAGGccaa -5'
miRNA: 3'- uaGgUGGCGCGGUCGGAGaa--GGCCAA- -5'
miRNA: 3'- -UAGGUGGCGCGGUCGGAGAAGGCCAA- -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 | |||||||
| 6791 | 5' | -60.8 | NC_001875.2 | + | 65744 | 0.66 | 0.580311 |
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Target: 5'- -cCCGCCGCGCgGGCCUCggCguauucgugcgcggCGGg- -3' miRNA: 3'- uaGGUGGCGCGgUCGGAGaaG--------------GCCaa -5' |
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| 6791 | 5' | -60.8 | NC_001875.2 | + | 94419 | 0.69 | 0.42978 |
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Target: 5'- -gCCgACUGCGCCacGGCCUCUUCCa--- -3' miRNA: 3'- uaGG-UGGCGCGG--UCGGAGAAGGccaa -5' |
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| 6791 | 5' | -60.8 | NC_001875.2 | + | 9049 | 0.71 | 0.346671 |
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Target: 5'- -cCgGCCGCGCCGGUUUCcgcgCCGGUUu -3' miRNA: 3'- uaGgUGGCGCGGUCGGAGaa--GGCCAA- -5' |
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| 6791 | 5' | -60.8 | NC_001875.2 | + | 71940 | 1.02 | 0.00207 |
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Target: 5'- uAUCCACCGCGCCAGCCUCUUCCGGUUu -3' miRNA: 3'- -UAGGUGGCGCGGUCGGAGAAGGCCAA- -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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