miRNA: 3'- -UUGCGcCUGCCAAGUGgCGc-----UACACa -5'
miRNA: 3'- -UUGCGcCugCCAa---GUGGCGCUACaCA- -5'
miRNA: 3'- uugCGCC-------UGCCAAGUGGCGcuACACa -5'
miRNA: 3'- -UUGCGCCUGCCAAGUGGCGCUACACA- -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 | |||||||
| 11385 | 5' | -56 | NC_003084.1 | + | 6465 | 0.66 | 0.854833 |
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Target: 5'- aGAUGCuGACGGUUCACgGCugcccaAUGUGc -3' miRNA: 3'- -UUGCGcCUGCCAAGUGgCGc-----UACACa -5' |
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| 11385 | 5' | -56 | NC_003084.1 | + | 60686 | 0.66 | 0.829938 |
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Target: 5'- uAACGCcGugGGUgauaCGCUGCGGUG-GUa -3' miRNA: 3'- -UUGCGcCugCCAa---GUGGCGCUACaCA- -5' |
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| 11385 | 5' | -56 | NC_003084.1 | + | 10867 | 0.67 | 0.79321 |
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Target: 5'- --gGCGGcugagcaGCGGUUCACCGUacUGUGc -3' miRNA: 3'- uugCGCC-------UGCCAAGUGGCGcuACACa -5' |
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| 11385 | 5' | -56 | NC_003084.1 | + | 67649 | 1.05 | 0.003328 |
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Target: 5'- cAACGCGGACGGUUCACCGCGAUGUGUg -3' miRNA: 3'- -UUGCGCCUGCCAAGUGGCGCUACACA- -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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