miRNA: 3'- -CAGGugCC-AGAcGUG-CG-------GGUCAGGGC- -5'
miRNA: 3'- caGGUGCCAGaCGUGC----GGGUCA-GGGC- -5'
miRNA: 3'- -CAGGUGCCAGACGUgCGGGuCAGGgc -5'
miRNA: 3'- -CAGGUGCCAGACGUGCGGGUCAGGGC- -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 | |||||||
| 172 | 3' | -60.5 | AC_000007.1 | + | 33727 | 0.67 | 0.290574 |
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Target: 5'- aGUCCugGGcUCUcCACuGUcauuguuCCAGUCCCGg -3' miRNA: 3'- -CAGGugCC-AGAcGUG-CG-------GGUCAGGGC- -5' |
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| 172 | 3' | -60.5 | AC_000007.1 | + | 6453 | 0.67 | 0.270137 |
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Target: 5'- -aCCGCGGUUgGCGCGugcaCCUGGUgCCCGa -3' miRNA: 3'- caGGUGCCAGaCGUGC----GGGUCA-GGGC- -5' |
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| 172 | 3' | -60.5 | AC_000007.1 | + | 12931 | 0.72 | 0.135145 |
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Target: 5'- gGUUUACGGUCUGCAgGCCUuGUCUa- -3' miRNA: 3'- -CAGGUGCCAGACGUgCGGGuCAGGgc -5' |
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| 172 | 3' | -60.5 | AC_000007.1 | + | 17211 | 1.09 | 0.000179 |
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Target: 5'- cGUCCACGGUCUGCACGCCCAGUCCCGg -3' miRNA: 3'- -CAGGUGCCAGACGUGCGGGUCAGGGC- -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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