miRNA: 3'- caCGGCGGC-GCGCC-----------CUACUUGGUAua -5'
miRNA: 3'- caCGGCGGCGcGCCCUA--------CUUGGUAUa -5'
miRNA: 3'- caCGGCGGCG-C-GCCCU---ACUUGGUaua -5'
miRNA: 3'- caCGGCGGCGcGCCCUACU----UGGUaua -5'
miRNA: 3'- -CACGGCGGCGCGCCCUACUUGGUAUA- -5'
Results 21 - 25 of 25 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 | |||||||
| 12846 | 5' | -57.9 | NC_003387.1 | + | 638 | 0.71 | 0.257988 |
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Target: 5'- -cGUCGCCGcCGCGGcagcgacgcccGAUGAACCAUu- -3' miRNA: 3'- caCGGCGGC-GCGCC-----------CUACUUGGUAua -5' |
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| 12846 | 5' | -57.9 | NC_003387.1 | + | 15895 | 0.71 | 0.257988 |
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Target: 5'- -cGCCGCCGC-CGGGAUcucacgcaGGAUCGUGa -3' miRNA: 3'- caCGGCGGCGcGCCCUA--------CUUGGUAUa -5' |
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| 12846 | 5' | -57.9 | NC_003387.1 | + | 23850 | 0.72 | 0.232597 |
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Target: 5'- -aGCCGCCGCaGuCGGGGccgUGGACCGg-- -3' miRNA: 3'- caCGGCGGCG-C-GCCCU---ACUUGGUaua -5' |
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| 12846 | 5' | -57.9 | NC_003387.1 | + | 9552 | 0.75 | 0.135457 |
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Target: 5'- -aGCCGCCGC-CGGGGUGGauucGCCAg-- -3' miRNA: 3'- caCGGCGGCGcGCCCUACU----UGGUaua -5' |
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| 12846 | 5' | -57.9 | NC_003387.1 | + | 14440 | 1.06 | 0.000709 |
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Target: 5'- cGUGCCGCCGCGCGGGAUGAACCAUAUg -3' miRNA: 3'- -CACGGCGGCGCGCCCUACUUGGUAUA- -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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