miRNA: 3'- gaCGGgAGc---GaCAGGACCUUCaGUCU- -5'
miRNA: 3'- -GAC-GGGAG--CGACAGGacCUUCAGUCU- -5'
miRNA: 3'- gaCGGGAgCGACAGGACCUu---CAg-UCU- -5'
miRNA: 3'- -GACGGG-------AGCGaCA-GGA--CCUUCAGUCU- -5'
miRNA: 3'- -GACGGGAGCGACAGGACCUUCAGUCU- -5'
Results 1 - 5 of 5 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 | |||||||
| 31753 | 3' | -56.4 | NC_006938.1 | + | 5603 | 0.66 | 0.684366 |
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Target: 5'- -cGCCgUCccacCcGUCCUGGAAGcCAGAc -3' miRNA: 3'- gaCGGgAGc---GaCAGGACCUUCaGUCU- -5' |
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| 31753 | 3' | -56.4 | NC_006938.1 | + | 36994 | 0.68 | 0.575855 |
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Target: 5'- uCUGaUCCUCauGCUGUCC--GAGGUCAGGg -3' miRNA: 3'- -GAC-GGGAG--CGACAGGacCUUCAGUCU- -5' |
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| 31753 | 3' | -56.4 | NC_006938.1 | + | 21775 | 0.69 | 0.501998 |
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Target: 5'- -gGCCCU-GCUGUCCUGGGcauuGUagGGAg -3' miRNA: 3'- gaCGGGAgCGACAGGACCUu---CAg-UCU- -5' |
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| 31753 | 3' | -56.4 | NC_006938.1 | + | 15088 | 0.69 | 0.470604 |
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Target: 5'- cCUGCCCcgaggucUCGC-GUaCCUccGGGAGUCAGGg -3' miRNA: 3'- -GACGGG-------AGCGaCA-GGA--CCUUCAGUCU- -5' |
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| 31753 | 3' | -56.4 | NC_006938.1 | + | 30543 | 1.09 | 0.000841 |
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Target: 5'- cCUGCCCUCGCUGUCCUGGAAGUCAGAg -3' miRNA: 3'- -GACGGGAGCGACAGGACCUUCAGUCU- -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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