miRNA: 3'- -UCCCGCaAUGGcCGU------------AGUCGCGGagu -5'
miRNA: 3'- -UCCC-GCAA-----------UG-GCCGU----AGUCGCGGAGu -5'
miRNA: 3'- ucCCGCAAUgGCCGuaGUCGCGGAGU- -5'
miRNA: 3'- -UCCCGCaa---UGGCCGUagUCGC-GGAGU- -5'
miRNA: 3'- -UCCCGCAAUGGCCGUAGUCGCGGAGU- -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 | |||||||
| 26011 | 3' | -58.4 | NC_005340.1 | + | 3934 | 0.67 | 0.312356 |
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Target: 5'- gAGGGUGaUACCuGCGacgggcgcauuaUCAGCGCCa-- -3' miRNA: 3'- -UCCCGCaAUGGcCGU------------AGUCGCGGagu -5' |
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| 26011 | 3' | -58.4 | NC_005340.1 | + | 8841 | 0.67 | 0.30449 |
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Target: 5'- cGGGGuUGUUucggagcugcgGCaCGGCGuuaaUCAGCGCCUUg -3' miRNA: 3'- -UCCC-GCAA-----------UG-GCCGU----AGUCGCGGAGu -5' |
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| 26011 | 3' | -58.4 | NC_005340.1 | + | 13028 | 0.69 | 0.221801 |
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Target: 5'- -cGGCGUUG-CGGC--CAGCGUCUCAg -3' miRNA: 3'- ucCCGCAAUgGCCGuaGUCGCGGAGU- -5' |
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| 26011 | 3' | -58.4 | NC_005340.1 | + | 2687 | 0.74 | 0.09462 |
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Target: 5'- cAGGGUGcagccACCGGCAagGGCGuCCUCAa -3' miRNA: 3'- -UCCCGCaa---UGGCCGUagUCGC-GGAGU- -5' |
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| 26011 | 3' | -58.4 | NC_005340.1 | + | 15574 | 1.08 | 0.000221 |
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Target: 5'- cAGGGCGUUACCGGCAUCAGCGCCUCAg -3' miRNA: 3'- -UCCCGCAAUGGCCGUAGUCGCGGAGU- -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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