miRNA: 3'- -UCGA---CCAAAGu-CAcACCUGAUGaGCG- -5'
miRNA: 3'- uCGACCAaAGUCa--CACCUGAug-------AGCG- -5'
miRNA: 3'- uCGACCAAAGUCACaCCu----GAU-GAGCG- -5'
miRNA: 3'- -UCGACCAAAGUCACACCUGAUGAGCG- -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 | |||||||
| 6109 | 3' | -50.9 | NC_001826.1 | + | 69001 | 0.66 | 0.982166 |
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Target: 5'- gAGCUgugGGUUUCuuGUuUGGACUAC-CGUc -3' miRNA: 3'- -UCGA---CCAAAGu-CAcACCUGAUGaGCG- -5' |
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| 6109 | 3' | -50.9 | NC_001826.1 | + | 7079 | 0.69 | 0.930658 |
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Target: 5'- uGCUGGUgUCAGacaGUGGGCUuggaucucaUCGCc -3' miRNA: 3'- uCGACCAaAGUCa--CACCUGAug-------AGCG- -5' |
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| 6109 | 3' | -50.9 | NC_001826.1 | + | 26021 | 0.73 | 0.752964 |
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Target: 5'- uGCUGGUUUCGGUGcGGcaacuCUGcCUUGCc -3' miRNA: 3'- uCGACCAAAGUCACaCCu----GAU-GAGCG- -5' |
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| 6109 | 3' | -50.9 | NC_001826.1 | + | 13350 | 1.14 | 0.003283 |
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Target: 5'- gAGCUGGUUUCAGUGUGGACUACUCGCa -3' miRNA: 3'- -UCGACCAAAGUCACACCUGAUGAGCG- -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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