miRNA: 3'- uacUCGGUCCaACUGGU------AGGAGUgau -5'
miRNA: 3'- -UACUCGGUCC---AACUGGU---AGG--AG--UGAU- -5'
miRNA: 3'- uACUCGGUCCAACUGGU-------AGGag-UGAu -5'
miRNA: 3'- -UACUCGGUCCAACUGGUAGGAGUGAU- -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 | |||||||
| 27717 | 5' | -54.2 | NC_005884.1 | + | 7737 | 0.66 | 0.641477 |
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Target: 5'- --aGGCCAGGgUGGCCAgcagagUCCUCAa-- -3' miRNA: 3'- uacUCGGUCCaACUGGU------AGGAGUgau -5' |
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| 27717 | 5' | -54.2 | NC_005884.1 | + | 43223 | 0.67 | 0.583765 |
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Target: 5'- cGUGGGCCAGGaaaUUGGCCAgggUCCaaUCagGCUGa -3' miRNA: 3'- -UACUCGGUCC---AACUGGU---AGG--AG--UGAU- -5' |
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| 27717 | 5' | -54.2 | NC_005884.1 | + | 17926 | 0.75 | 0.191201 |
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Target: 5'- cUGAGCCAGGUUGACCAggcuggaUCCaaaGCUc -3' miRNA: 3'- uACUCGGUCCAACUGGU-------AGGag-UGAu -5' |
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| 27717 | 5' | -54.2 | NC_005884.1 | + | 9755 | 1.05 | 0.001263 |
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Target: 5'- gAUGAGCCAGGUUGACCAUCCUCACUAg -3' miRNA: 3'- -UACUCGGUCCAACUGGUAGGAGUGAU- -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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