miRNA: 3'- aGCC-CCUGCCGUCGuccGGC-GCCUCG- -5'
miRNA: 3'- aGCCCCUGC-CGu-------CGuCCGg---CGCCUCG- -5'
miRNA: 3'- aGCCccugCCGuCGUCCGGCgCCUCG- -5'
miRNA: 3'- -AGCcCCUGCC-GUCGuc--CGGCGCCUCG- -5'
miRNA: 3'- -AGCcc--CUGCCGuCGUCCGgCGCCUCG- -5'
Results 1 - 5 of 5 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 | |||||||
| 8907 | 3' | -64.1 | NC_002484.1 | + | 31866 | 0.66 | 0.294233 |
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Target: 5'- cUGGaGGGCGGCAGCu--UCGaUGGGGCa -3' miRNA: 3'- aGCC-CCUGCCGUCGuccGGC-GCCUCG- -5' |
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| 8907 | 3' | -64.1 | NC_002484.1 | + | 9748 | 0.66 | 0.287373 |
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Target: 5'- gCGGGGACGcGCcaaggaucGC-GGUaacaGCGGGGCu -3' miRNA: 3'- aGCCCCUGC-CGu-------CGuCCGg---CGCCUCG- -5' |
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| 8907 | 3' | -64.1 | NC_002484.1 | + | 51810 | 0.7 | 0.175461 |
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Target: 5'- aUGGccaaGGC-GCAGGCCGgGGAGCa -3' miRNA: 3'- aGCCccugCCGuCGUCCGGCgCCUCG- -5' |
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| 8907 | 3' | -64.1 | NC_002484.1 | + | 4944 | 0.7 | 0.171033 |
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Target: 5'- gUCGcGGAUGGuCAGUcgacGCUGCGGAGCg -3' miRNA: 3'- -AGCcCCUGCC-GUCGuc--CGGCGCCUCG- -5' |
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| 8907 | 3' | -64.1 | NC_002484.1 | + | 29313 | 0.7 | 0.162476 |
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Target: 5'- cUCGaacuGGCGGC-GCGGGCgGCGGGGUa -3' miRNA: 3'- -AGCcc--CUGCCGuCGUCCGgCGCCUCG- -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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