miRNA: 3'- -UGAGCUCACCA--------------ACUGCCA---------GCCUGuGG- -5'
miRNA: 3'- -UG-AGCUCaCCaACUGCCAgCCUGU-GG- -5'
miRNA: 3'- uGAGCUCACCaa-CUGCCa-----GCCugUGG- -5'
miRNA: 3'- -UGAGCUCACCAACUGCCAGCCUGUGG- -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 | |||||||
| 15290 | 3' | -54.2 | NC_003849.1 | + | 4749 | 0.66 | 0.201416 |
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Target: 5'- gGCUUGGGUGGUcugguccagggcaaUGACGGUgccgagcagUGGGC-CUu -3' miRNA: 3'- -UGAGCUCACCA--------------ACUGCCA---------GCCUGuGG- -5' |
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| 15290 | 3' | -54.2 | NC_003849.1 | + | 814 | 0.7 | 0.102826 |
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Target: 5'- gGCgUUGAGcGG-UGACGGUgGGGCAgCCg -3' miRNA: 3'- -UG-AGCUCaCCaACUGCCAgCCUGU-GG- -5' |
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| 15290 | 3' | -54.2 | NC_003849.1 | + | 4846 | 0.72 | 0.071012 |
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Target: 5'- cCUCGAGUGGgagGGCGGagacuaCGGuuACCg -3' miRNA: 3'- uGAGCUCACCaa-CUGCCa-----GCCugUGG- -5' |
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| 15290 | 3' | -54.2 | NC_003849.1 | + | 744 | 1.11 | 0.000038 |
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Target: 5'- aACUCGAGUGGUUGACGGUCGGACACCu -3' miRNA: 3'- -UGAGCUCACCAACUGCCAGCCUGUGG- -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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