miRNA: 3'- -CGCg---GCCUGCUacaUAACUAGCGGGu -5'
miRNA: 3'- -CGCGG--CCUGCUa---------CAUAACU--AGCGgGU- -5'
miRNA: 3'- -CGCg--GCC--------UGCUACAUAACuAGCG-GGU- -5'
miRNA: 3'- -CGCGGCcUG-CUACAUA----ACUAGCGggu -5'
miRNA: 3'- -CGCGGCCUGCUACAUAACUAGCGGGU- -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 | |||||||
| 22823 | 3' | -53.5 | NC_005135.1 | + | 150885 | 0.66 | 0.980762 |
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Target: 5'- cGUGgucaCGGAUGAacgGUUGAUCGCCUu -3' miRNA: 3'- -CGCg---GCCUGCUacaUAACUAGCGGGu -5' |
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| 22823 | 3' | -53.5 | NC_005135.1 | + | 109955 | 0.66 | 0.980762 |
|
Target: 5'- uGCGCCauGGAUGAgccgaauaacGUGUUGAugUCGCgCAa -3' miRNA: 3'- -CGCGG--CCUGCUa---------CAUAACU--AGCGgGU- -5' |
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| 22823 | 3' | -53.5 | NC_005135.1 | + | 95901 | 0.66 | 0.973585 |
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Target: 5'- gGCGaggCGGcucacccuGCGAUGUAUUG-UCGCuCCAc -3' miRNA: 3'- -CGCg--GCC--------UGCUACAUAACuAGCG-GGU- -5' |
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| 22823 | 3' | -53.5 | NC_005135.1 | + | 72521 | 0.68 | 0.949686 |
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Target: 5'- uGCGCCGuGCaGGUGUAUggcaUGAUCGCa-- -3' miRNA: 3'- -CGCGGCcUG-CUACAUA----ACUAGCGggu -5' |
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| 22823 | 3' | -53.5 | NC_005135.1 | + | 87835 | 1.11 | 0.004625 |
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Target: 5'- aGCGCCGGACGAUGUAUUGAUCGCCCAu -3' miRNA: 3'- -CGCGGCCUGCUACAUAACUAGCGGGU- -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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