miRNA: 3'- aACCuuGC-UGGUGGGUCU---------------CGGAGGGU- -5'
miRNA: 3'- -AACCU---UGCUGGUGggUCUCGgAGGGu -5'
miRNA: 3'- aACCU-------UGCUGG--UGGgUCUCGGAGGGu -5'
miRNA: 3'- -AACCUUGCUGGUgGGUCUCGGAGGGU- -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 | |||||||
| 17985 | 3' | -58.8 | NC_004665.1 | + | 20121 | 0.67 | 0.348178 |
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Target: 5'- aUGGucCGuACCAUCCAGAaugguaagucggccaGCUUCCCGg -3' miRNA: 3'- aACCuuGC-UGGUGGGUCU---------------CGGAGGGU- -5' |
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| 17985 | 3' | -58.8 | NC_004665.1 | + | 27115 | 0.69 | 0.247569 |
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Target: 5'- cUUGGAuagACGACCAC--GGAGCgUCCCu -3' miRNA: 3'- -AACCU---UGCUGGUGggUCUCGgAGGGu -5' |
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| 17985 | 3' | -58.8 | NC_004665.1 | + | 29334 | 0.71 | 0.183543 |
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Target: 5'- aUGGGaagcucaACGACCucACUgAGAGCCUCCUg -3' miRNA: 3'- aACCU-------UGCUGG--UGGgUCUCGGAGGGu -5' |
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| 17985 | 3' | -58.8 | NC_004665.1 | + | 22402 | 0.94 | 0.003312 |
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Target: 5'- cUUGGAACGACCA-CCAGAGCCUCCCAg -3' miRNA: 3'- -AACCUUGCUGGUgGGUCUCGGAGGGU- -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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