miRNA: 3'- aucGGGAGCaCCGC--UUGGUGG----GCGGc -5'
miRNA: 3'- aUCGGGAGCACCG---CUUGg------UGgGCGGc -5'
miRNA: 3'- aUCGGGagCACCGcUUGGUgGGCGGC- -5'
miRNA: 3'- aUCGGGagca-CCG--------------CUUGGUGGGCGGC- -5'
miRNA: 3'- aUCGGGaGCACCG-CUUGG---UGGGcGGc -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 | |||||||
| 30635 | 3' | -61.7 | NC_006549.1 | + | 115025 | 0.66 | 0.639921 |
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Target: 5'- --aCCCUCGcGGCGugGACCGCCuuuaCGCCc -3' miRNA: 3'- aucGGGAGCaCCGC--UUGGUGG----GCGGc -5' |
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| 30635 | 3' | -61.7 | NC_006549.1 | + | 113807 | 0.66 | 0.639921 |
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Target: 5'- cGGCCCUCGUGGUccuGAGCaguuuuuGCgCGCUc -3' miRNA: 3'- aUCGGGAGCACCG---CUUGg------UGgGCGGc -5' |
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| 30635 | 3' | -61.7 | NC_006549.1 | + | 74840 | 0.67 | 0.590309 |
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Target: 5'- aGGCCCggGUGGCuAAUCA-CUGCCGg -3' miRNA: 3'- aUCGGGagCACCGcUUGGUgGGCGGC- -5' |
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| 30635 | 3' | -61.7 | NC_006549.1 | + | 6609 | 0.68 | 0.519348 |
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Target: 5'- gGGUCCcacugGGCcgcagggagacgcaGGACCACCCGCCGa -3' miRNA: 3'- aUCGGGagca-CCG--------------CUUGGUGGGCGGC- -5' |
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| 30635 | 3' | -61.7 | NC_006549.1 | + | 11127 | 0.71 | 0.364994 |
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Target: 5'- aAGCCC-CGUGGCgGAACCcaaACCCaCCa -3' miRNA: 3'- aUCGGGaGCACCG-CUUGG---UGGGcGGc -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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