miRNA: 3'- aagCCUUUugUCAAg------GGGAGACCaaa -5'
miRNA: 3'- aAGCCUUUUG---------UCAAGGGGAGACCAAA- -5'
miRNA: 3'- aaGCCUuuUGUCAAGG-GGAGACCAAA- -5'
miRNA: 3'- -AAGCCUUUUGUCAAGGGGAGACCAAA- -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 | |||||||
| 21016 | 3' | -50.6 | NC_004735.1 | + | 61833 | 0.66 | 0.98358 |
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Target: 5'- --gGGGAAugGGUUaccugaaCCCUCUGGa-- -3' miRNA: 3'- aagCCUUUugUCAAg------GGGAGACCaaa -5' |
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| 21016 | 3' | -50.6 | NC_004735.1 | + | 113229 | 0.71 | 0.857611 |
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Target: 5'- aUCGGAAGAUauaccuucaAGUUUUUCUCUGGUUUc -3' miRNA: 3'- aAGCCUUUUG---------UCAAGGGGAGACCAAA- -5' |
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| 21016 | 3' | -50.6 | NC_004735.1 | + | 83146 | 0.72 | 0.794402 |
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Target: 5'- -cCGGGuuAUGGUUCCuCUUCUGGUUUa -3' miRNA: 3'- aaGCCUuuUGUCAAGG-GGAGACCAAA- -5' |
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| 21016 | 3' | -50.6 | NC_004735.1 | + | 82953 | 1.02 | 0.016341 |
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Target: 5'- cUUCGGAAAACAGUUCCCCUCUGGUUUc -3' miRNA: 3'- -AAGCCUUUUGUCAAGGGGAGACCAAA- -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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