miRNA: 3'- cCUGAaaUAGGCGG---ACCGG--CAGUUGU- -5'
miRNA: 3'- cCUGAAaUAGGCgGACcGGCAGUUGu -5'
miRNA: 3'- -CCUGaaaUAGGCGGACC--GGCaGUUGu -5'
miRNA: 3'- -CCUGaaauaGGCGGaC-CGGCAGUUGu -5'
miRNA: 3'- -CCUGAAAUAGGCGGACCGGCAGUUGU- -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 | |||||||
| 8833 | 5' | -52.1 | NC_002484.1 | + | 35441 | 0.66 | 0.892971 |
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Target: 5'- uGGCU--AUUCGCCggaUGGCCuaGUCGGCGa -3' miRNA: 3'- cCUGAaaUAGGCGG---ACCGG--CAGUUGU- -5' |
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| 8833 | 5' | -52.1 | NC_002484.1 | + | 46505 | 0.67 | 0.844464 |
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Target: 5'- cGGCUUcAUCCGgCUGaUCGUCGACu -3' miRNA: 3'- cCUGAAaUAGGCgGACcGGCAGUUGu -5' |
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| 8833 | 5' | -52.1 | NC_002484.1 | + | 51433 | 0.69 | 0.746301 |
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Target: 5'- aGGACg--AUCCGUCUGGuuCCGcCAAUc -3' miRNA: 3'- -CCUGaaaUAGGCGGACC--GGCaGUUGu -5' |
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| 8833 | 5' | -52.1 | NC_002484.1 | + | 4880 | 0.7 | 0.669738 |
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Target: 5'- aGGGCg----CCGCCaGaGCCGUCGAUg -3' miRNA: 3'- -CCUGaaauaGGCGGaC-CGGCAGUUGu -5' |
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| 8833 | 5' | -52.1 | NC_002484.1 | + | 27687 | 1.11 | 0.001569 |
|
Target: 5'- aGGACUUUAUCCGCCUGGCCGUCAACAc -3' miRNA: 3'- -CCUGAAAUAGGCGGACCGGCAGUUGU- -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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