miRNA: 3'- gUGGCGACAGACGccGUGCGGU---CGUA- -5'
miRNA: 3'- -GUGGC-------GACAGAC-GCCG--------------UGCGGUCGua -5'
miRNA: 3'- -GUG-GCGACAG-------ACGCCGUgC-GGUCGUa -5'
miRNA: 3'- -GUGGCGACAGACGCCGUGCGGUCGUA- -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 | |||||||
| 12738 | 3' | -60.5 | NC_003356.1 | + | 30510 | 0.67 | 0.299592 |
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Target: 5'- aGCUGUUGUCUGC--CACGCCAuauGCAUu -3' miRNA: 3'- gUGGCGACAGACGccGUGCGGU---CGUA- -5' |
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| 12738 | 3' | -60.5 | NC_003356.1 | + | 29626 | 0.68 | 0.241715 |
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Target: 5'- uCACCGaaaggauCUGUCUGaCGGUgacgucaaccauacGCGCCAGCu- -3' miRNA: 3'- -GUGGC-------GACAGAC-GCCG--------------UGCGGUCGua -5' |
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| 12738 | 3' | -60.5 | NC_003356.1 | + | 21751 | 0.68 | 0.231199 |
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Target: 5'- uCGCgCGCUGUUuucgcuuUGUGGCAgGgCCAGCAc -3' miRNA: 3'- -GUG-GCGACAG-------ACGCCGUgC-GGUCGUa -5' |
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| 12738 | 3' | -60.5 | NC_003356.1 | + | 35392 | 1.04 | 0.00039 |
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Target: 5'- uCACCGCUGUCUGCGGCACGCCAGCAUc -3' miRNA: 3'- -GUGGCGACAGACGCCGUGCGGUCGUA- -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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