miRNA: 3'- -ACGUCCCC----ACACGGGAa-----UUGU-------GGGUu -5'
miRNA: 3'- -ACGu-CCCCACa-------CGGGAAUU-GUGGGuu -5'
miRNA: 3'- aCGUccCCACACgGGAAUUGUGGGuu -5'
miRNA: 3'- -ACGUCCCCACACGGGAAUUGUGGGUU- -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 | |||||||
| 6198 | 5' | -56.7 | NC_001844.1 | + | 89311 | 0.66 | 0.808359 |
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Target: 5'- aUGCGGGGGcaguUGUGUCCUgauuggAACGauuugucCCCAu -3' miRNA: 3'- -ACGUCCCC----ACACGGGAa-----UUGU-------GGGUu -5' |
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| 6198 | 5' | -56.7 | NC_001844.1 | + | 117297 | 0.68 | 0.742831 |
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Target: 5'- aUGUuuGGGGUGgacgacgcGCCCUUGGcCACCCc- -3' miRNA: 3'- -ACGu-CCCCACa-------CGGGAAUU-GUGGGuu -5' |
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| 6198 | 5' | -56.7 | NC_001844.1 | + | 64495 | 0.68 | 0.73286 |
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Target: 5'- aGCGuaGGUGUGgUCUUGACACCCc- -3' miRNA: 3'- aCGUccCCACACgGGAAUUGUGGGuu -5' |
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| 6198 | 5' | -56.7 | NC_001844.1 | + | 2590 | 1.05 | 0.003016 |
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Target: 5'- cUGCAGGGGUGUGCCCUUAACACCCAAc -3' miRNA: 3'- -ACGUCCCCACACGGGAAUUGUGGGUU- -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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