miRNA: 3'- -GUUUGa--GGGA-CG------------CUGUGAGCCCCGCG- -5'
miRNA: 3'- gUUUGaGGGa--CGCUG--UGAG----CCCCGCG- -5'
miRNA: 3'- gUUUGAGgGACGCUGugagCCCCGCG- -5'
miRNA: 3'- -GUUUGAGGGACGCUGUGAGCCCCGCG- -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 | |||||||
| 27940 | 3' | -57.1 | NC_005886.2 | + | 29707 | 0.66 | 0.548455 |
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Target: 5'- uCGGGCguaCCUUcGCcgucgcacuucgGGCAUUCGGGGUGCg -3' miRNA: 3'- -GUUUGa--GGGA-CG------------CUGUGAGCCCCGCG- -5' |
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| 27940 | 3' | -57.1 | NC_005886.2 | + | 24917 | 0.66 | 0.548455 |
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Target: 5'- aAAACgCCCcgcGCGACcgGCUCgcgcGGGGCGUu -3' miRNA: 3'- gUUUGaGGGa--CGCUG--UGAG----CCCCGCG- -5' |
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| 27940 | 3' | -57.1 | NC_005886.2 | + | 8284 | 0.68 | 0.455514 |
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Target: 5'- aGAGCUUgCUGCGAUg---GGGGUGCg -3' miRNA: 3'- gUUUGAGgGACGCUGugagCCCCGCG- -5' |
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| 27940 | 3' | -57.1 | NC_005886.2 | + | 27803 | 1.11 | 0.000373 |
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Target: 5'- uCAAACUCCCUGCGACACUCGGGGCGCa -3' miRNA: 3'- -GUUUGAGGGACGCUGUGAGCCCCGCG- -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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