miRNA: 3'- acUCCaCCGUGC-GCCaGUCGCAGaac -5'
miRNA: 3'- aCUCCACCGUGc---GCC--AGUCGCaGAac -5'
miRNA: 3'- aCUCCa-CCGUGCG---CCAG-UCGCAgaac -5'
miRNA: 3'- aCUCC---ACCGUGCGCCaGUCGCaGAac -5'
miRNA: 3'- acuCCACCGUGCGCCa--GUCGCagaac -5'
Results 21 - 25 of 25 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand |
Start Position
|
R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 25685 | 5' | -57.1 | NC_005337.1 | + | 98484 | 0.66 | 0.819838 |
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Target: 5'- -cAGG-GGCGCGcCGG-CGGCGUCc-- -3' miRNA: 3'- acUCCaCCGUGC-GCCaGUCGCAGaac -5' |
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| 25685 | 5' | -57.1 | NC_005337.1 | + | 100591 | 0.68 | 0.716397 |
|
Target: 5'- gGAGGUGGCGCccgcCGGccUCGGCGcCUc- -3' miRNA: 3'- aCUCCACCGUGc---GCC--AGUCGCaGAac -5' |
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| 25685 | 5' | -57.1 | NC_005337.1 | + | 109378 | 0.68 | 0.716397 |
|
Target: 5'- gGAGGcgGGCACGCgcgGGUCuGGCGUg--- -3' miRNA: 3'- aCUCCa-CCGUGCG---CCAG-UCGCAgaac -5' |
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| 25685 | 5' | -57.1 | NC_005337.1 | + | 122395 | 0.68 | 0.746001 |
|
Target: 5'- cGGGGcagUGGUACGUGGgCAGCGcCUc- -3' miRNA: 3'- aCUCC---ACCGUGCGCCaGUCGCaGAac -5' |
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| 25685 | 5' | -57.1 | NC_005337.1 | + | 127882 | 0.69 | 0.686138 |
|
Target: 5'- --uGGUGGCGCGCGGcgcCGGCGa---- -3' miRNA: 3'- acuCCACCGUGCGCCa--GUCGCagaac -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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