miRNA: 3'- aGUAG-CCUGa---CAC-------------UGGgCGGGGCCCc -5'
miRNA: 3'- -AGUAGCc--UGACACU----------GGGCGG---------------GGCCCC- -5'
miRNA: 3'- aguaGCCugACACUGg----GCGGGGCCCC- -5'
miRNA: 3'- -AGUAGCCUGACACUGGGCGGGGCCCC- -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 | |||||||
| 21770 | 3' | -60.7 | NC_004813.1 | + | 36101 | 0.66 | 0.506271 |
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Target: 5'- aCGUCaGGACgcccGUGaagccauaaugcuGCUgGCCCCGGGa -3' miRNA: 3'- aGUAG-CCUGa---CAC-------------UGGgCGGGGCCCc -5' |
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| 21770 | 3' | -60.7 | NC_004813.1 | + | 46779 | 0.68 | 0.365348 |
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Target: 5'- gUCAUCGuaaACUGUGAcgguuaccguCCCGCUggcauaacuguuauuCCGGGGa -3' miRNA: 3'- -AGUAGCc--UGACACU----------GGGCGG---------------GGCCCC- -5' |
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| 21770 | 3' | -60.7 | NC_004813.1 | + | 34468 | 0.74 | 0.153431 |
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Target: 5'- ---cUGGugUGUGGCauacgUGCCCCGGGGa -3' miRNA: 3'- aguaGCCugACACUGg----GCGGGGCCCC- -5' |
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| 21770 | 3' | -60.7 | NC_004813.1 | + | 27278 | 1.11 | 0.00029 |
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Target: 5'- aUCAUCGGACUGUGACCCGCCCCGGGGg -3' miRNA: 3'- -AGUAGCCUGACACUGGGCGGGGCCCC- -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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