miRNA: 3'- aGCGGa-CCGA-CCAG---------AGGCACgaCGUg -5'
miRNA: 3'- -AGCGGa------CCGaCCag-AGG-CACGAC-GUG- -5'
miRNA: 3'- agCGGACC---GACCaGAGGCacGACGUG- -5'
miRNA: 3'- -AGCGGACCGACCAGAGGCACGACGUG- -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 | |||||||
| 18496 | 3' | -60 | NC_004681.1 | + | 6611 | 0.66 | 0.529292 |
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Target: 5'- gCGCCgcGGCUcGGUCuuccccgagUCCGUGgaGCGa -3' miRNA: 3'- aGCGGa-CCGA-CCAG---------AGGCACgaCGUg -5' |
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| 18496 | 3' | -60 | NC_004681.1 | + | 45374 | 0.66 | 0.509075 |
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Target: 5'- uUCGCCggucacgGGCgGGgcgUCCgGUGCUGcCACg -3' miRNA: 3'- -AGCGGa------CCGaCCag-AGG-CACGAC-GUG- -5' |
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| 18496 | 3' | -60 | NC_004681.1 | + | 129 | 0.67 | 0.46007 |
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Target: 5'- -aGCCUGGaaaCUGG-CUCUGacCUGCACa -3' miRNA: 3'- agCGGACC---GACCaGAGGCacGACGUG- -5' |
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| 18496 | 3' | -60 | NC_004681.1 | + | 54698 | 1.09 | 0.000484 |
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Target: 5'- aUCGCCUGGCUGGUCUCCGUGCUGCACc -3' miRNA: 3'- -AGCGGACCGACCAGAGGCACGACGUG- -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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