miRNA: 3'- -GGGCAcCAGC-----------CGCCCGGAa-AGCCGaa -5'
miRNA: 3'- -GGGCACCaGCCGCc-CGGaaAGCCGaa -5'
miRNA: 3'- -GGGCACCa---GCCGCCCGGaaa-GCCGaa -5'
miRNA: 3'- -GGGCACCAGCCGCCCGGAAAGCCGAA- -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 | |||||||
| 12654 | 3' | -60.8 | NC_003345.1 | + | 38787 | 0.66 | 0.532131 |
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Target: 5'- uUCCGUuGUCGuacauccgcuuGCGGGCUUcgUCGGCg- -3' miRNA: 3'- -GGGCAcCAGC-----------CGCCCGGAa-AGCCGaa -5' |
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| 12654 | 3' | -60.8 | NC_003345.1 | + | 74853 | 0.66 | 0.492678 |
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Target: 5'- uCCCGUGGaCGGCGaaGCCg-UCGGUc- -3' miRNA: 3'- -GGGCACCaGCCGCc-CGGaaAGCCGaa -5' |
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| 12654 | 3' | -60.8 | NC_003345.1 | + | 53357 | 0.7 | 0.298795 |
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Target: 5'- gCUCGUGGauucCGGCGGGUCggugCGGCc- -3' miRNA: 3'- -GGGCACCa---GCCGCCCGGaaa-GCCGaa -5' |
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| 12654 | 3' | -60.8 | NC_003345.1 | + | 59334 | 1.06 | 0.000721 |
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Target: 5'- aCCCGUGGUCGGCGGGCCUUUCGGCUUc -3' miRNA: 3'- -GGGCACCAGCCGCCCGGAAAGCCGAA- -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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