miRNA: 3'- gCGGGuUGCAcCCCGUGc---------UUGGGUGC- -5'
miRNA: 3'- gCGGGuUGCAcCCCGUGc---------UUGGGUGC- -5'
miRNA: 3'- -GCGGGUUGCACCCCGugCUuggGUGC- -5'
miRNA: 3'- -GCGGGUUGCACCCCGUGCUUGGGUGC- -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 | |||||||
| 3348 | 5' | -58.9 | NC_001550.1 | + | 8308 | 0.71 | 0.054424 |
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Target: 5'- uGCCCcACGUuGGGCGCcaacugucccGACCCGCGg -3' miRNA: 3'- gCGGGuUGCAcCCCGUGc---------UUGGGUGC- -5' |
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| 3348 | 5' | -58.9 | NC_001550.1 | + | 149 | 0.71 | 0.051003 |
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Target: 5'- aGCCCcACGUuGGGCGCcaacugucccGACCCGCGg -3' miRNA: 3'- gCGGGuUGCAcCCCGUGc---------UUGGGUGC- -5' |
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| 3348 | 5' | -58.9 | NC_001550.1 | + | 125 | 0.81 | 0.007048 |
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Target: 5'- gCGCCCAACGUGGGGCugGA---UACGa -3' miRNA: 3'- -GCGGGUUGCACCCCGugCUuggGUGC- -5' |
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| 3348 | 5' | -58.9 | NC_001550.1 | + | 8284 | 1.09 | 0.000031 |
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Target: 5'- gCGCCCAACGUGGGGCACGAACCCACGa -3' miRNA: 3'- -GCGGGUUGCACCCCGUGCUUGGGUGC- -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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