miRNA: 3'- -GGACGGCCag-------GGgCGUaUCuuCCACG- -5'
miRNA: 3'- -GGacGGCCa-GGG-GCGUaUCU--UCCACG- -5'
miRNA: 3'- -GGACgGCCAG-GGGCGUa---UCU-------------UCCACG- -5'
miRNA: 3'- -GGACGGCCAGGGGCGUAUCUUCCACG- -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 | |||||||
| 6165 | 3' | -57 | NC_001837.1 | + | 5826 | 0.66 | 0.194225 |
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Target: 5'- uCCUGCUGGgaaugucagCCgGCA-GGgcGGUGCa -3' miRNA: 3'- -GGACGGCCag-------GGgCGUaUCuuCCACG- -5' |
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| 6165 | 3' | -57 | NC_001837.1 | + | 1921 | 0.68 | 0.12629 |
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Target: 5'- aCCccCCGGcgCCCaCGCAgAGAauGGGUGCg -3' miRNA: 3'- -GGacGGCCa-GGG-GCGUaUCU--UCCACG- -5' |
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| 6165 | 3' | -57 | NC_001837.1 | + | 3330 | 0.69 | 0.118228 |
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Target: 5'- gCCUG-UGGUCgCCCGUAggggAGAcgaagugcucauaGGGUGCu -3' miRNA: 3'- -GGACgGCCAG-GGGCGUa---UCU-------------UCCACG- -5' |
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| 6165 | 3' | -57 | NC_001837.1 | + | 1476 | 1.14 | 2.1e-05 |
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Target: 5'- aCCUGCCGGUCCCCGCAUAGAAGGUGCa -3' miRNA: 3'- -GGACGGCCAGGGGCGUAUCUUCCACG- -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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