miRNA: 3'- uuCUACGC---UCG----GAACU--UgUGCCGAAG- -5'
miRNA: 3'- uuCUACGCU-CG----GAACUUG-UGCCGaag -5'
miRNA: 3'- -UUCUACG----CUCGGAACU----UGugCC-GAAG- -5'
miRNA: 3'- -UUCUACGCUCGGAACUUGUGCCGAAG- -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 | |||||||
| 27955 | 3' | -52.4 | NC_005886.2 | + | 22086 | 0.66 | 0.796915 |
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Target: 5'- -cGAUGCGuucGGCaauaCUUGAuuGgACGGCUUCu -3' miRNA: 3'- uuCUACGC---UCG----GAACU--UgUGCCGAAG- -5' |
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| 27955 | 3' | -52.4 | NC_005886.2 | + | 2665 | 0.66 | 0.77612 |
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Target: 5'- -uGAUGCGAuGCuguaCUUGAACgGCGGCg-- -3' miRNA: 3'- uuCUACGCU-CG----GAACUUG-UGCCGaag -5' |
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| 27955 | 3' | -52.4 | NC_005886.2 | + | 30434 | 0.69 | 0.594813 |
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Target: 5'- aAAGAUGCuguaGAGCCUUGAuuuuAUugGGuCUUUu -3' miRNA: 3'- -UUCUACG----CUCGGAACU----UGugCC-GAAG- -5' |
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| 27955 | 3' | -52.4 | NC_005886.2 | + | 45036 | 1.06 | 0.001861 |
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Target: 5'- uAAGAUGCGAGCCUUGAACACGGCUUCc -3' miRNA: 3'- -UUCUACGCUCGGAACUUGUGCCGAAG- -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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