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miRNA: 3'- cugGCCGACGUGCC---------GCGAGGUAGCaa -5'
miRNA: 3'- cUGGCCGaCGUGCCGCga-GGUAGcaa -5'
miRNA: 3'- cuGGCCGACGUGcCGCG--------------AGGUAGCaa -5'
miRNA: 3'- -CUGGCCGACGUGCCGCGAGGUAGCAA- -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#
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P value |
| Predicted miRNA align pattern | |||||||
| 2333 | 5' | -60.1 | NC_001416.1 | + | 8619 | 0.66 | 0.394869 |
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Target: 5'- --aCGGCUGCACGGaguucaguaUGUUUCAUCGc- -3' miRNA: 3'- cugGCCGACGUGCC---------GCGAGGUAGCaa -5' |
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| 2333 | 5' | -60.1 | NC_001416.1 | + | 4721 | 0.69 | 0.255067 |
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Target: 5'- cACCGGCaGCACGGCGaugCCGUUc-- -3' miRNA: 3'- cUGGCCGaCGUGCCGCga-GGUAGcaa -5' |
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| 2333 | 5' | -60.1 | NC_001416.1 | + | 5494 | 0.7 | 0.222455 |
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Target: 5'- -uCCGGCUGCGCcGCGCuggcguucucgcccUCCGUCGc- -3' miRNA: 3'- cuGGCCGACGUGcCGCG--------------AGGUAGCaa -5' |
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| 2333 | 5' | -60.1 | NC_001416.1 | + | 4393 | 1.04 | 0.00053 |
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Target: 5'- aGACCGGCUGCACGGCGCUCCAUCGUUu -3' miRNA: 3'- -CUGGCCGACGUGCCGCGAGGUAGCAA- -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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