miRNA: 3'- -CCGGUGugGGa--CGGUcCGUCCCaGAa -5'
miRNA: 3'- -CCGG---UGUGggACGGUC----CGUCCCAGAa -5'
miRNA: 3'- -CCGGuGUGGgaCGGUCCGUCC-CAGaa -5'
miRNA: 3'- -CCGgUG-------UGGGACGGuCCGUCCCAgAa -5'
miRNA: 3'- -CCGGUGUGGGACGGUCCGUCCCAGAA- -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 | |||||||
| 13619 | 5' | -61.5 | NC_003460.1 | + | 2238 | 0.66 | 0.040562 |
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Target: 5'- uGGUCAUugCCcugGCCAuGCAGGGcCUc -3' miRNA: 3'- -CCGGUGugGGa--CGGUcCGUCCCaGAa -5' |
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| 13619 | 5' | -61.5 | NC_003460.1 | + | 2351 | 0.68 | 0.027863 |
|
Target: 5'- gGGCCaggGCAUuuUGUCGGgauuGCAGGGUCUg -3' miRNA: 3'- -CCGG---UGUGggACGGUC----CGUCCCAGAa -5' |
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| 13619 | 5' | -61.5 | NC_003460.1 | + | 5683 | 0.7 | 0.01783 |
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Target: 5'- aGGCC-CGCC--GCCAGGCGGGuGUCc- -3' miRNA: 3'- -CCGGuGUGGgaCGGUCCGUCC-CAGaa -5' |
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| 13619 | 5' | -61.5 | NC_003460.1 | + | 3740 | 0.74 | 0.00891 |
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Target: 5'- gGGCgAUgucgaagACCCUGCCuGGCAGGGUgUg -3' miRNA: 3'- -CCGgUG-------UGGGACGGuCCGUCCCAgAa -5' |
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| 13619 | 5' | -61.5 | NC_003460.1 | + | 3782 | 1.06 | 9e-06 |
|
Target: 5'- gGGCCACACCCUGCCAGGCAGGGUCUUc -3' miRNA: 3'- -CCGGUGUGGGACGGUCCGUCCCAGAA- -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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