miRNA: 3'- cAGCGCGUGCU-----------AGCG-C---------AUCGUCAGCa -5'
miRNA: 3'- -CAGCG------CGUGCUAGCGCAUcGUCaGCa -5'
miRNA: 3'- cAGCGCGuGCUAGCG---------------CAUCG---UCA-GCA- -5'
miRNA: 3'- -CAGC-GCGUGCUaGC-GCA--UCGUC----AGCA- -5'
Results 21 - 24 of 24 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 | |||||||
| 24839 | 3' | -55.7 | NC_005284.1 | + | 17690 | 0.66 | 0.669512 |
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Target: 5'- aUCGUGCGCGAcgcccugaaucUCGCcGgcgcgucgaUGGCGGUCGa -3' miRNA: 3'- cAGCGCGUGCU-----------AGCG-C---------AUCGUCAGCa -5' |
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| 24839 | 3' | -55.7 | NC_005284.1 | + | 37452 | 0.66 | 0.691274 |
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Target: 5'- cGUCGCaguaacGCGCGAUUGCGUA-CAG-CGc -3' miRNA: 3'- -CAGCG------CGUGCUAGCGCAUcGUCaGCa -5' |
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| 24839 | 3' | -55.7 | NC_005284.1 | + | 24436 | 0.66 | 0.695602 |
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Target: 5'- cUCGCGCuCGAUCGCcucgaucucaacgucGUAGCcgcGGUaCGUg -3' miRNA: 3'- cAGCGCGuGCUAGCG---------------CAUCG---UCA-GCA- -5' |
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| 24839 | 3' | -55.7 | NC_005284.1 | + | 45157 | 0.66 | 0.702075 |
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Target: 5'- gGUCGaCGCACGG-CGaCGUcgGGCAGgagaUCGUg -3' miRNA: 3'- -CAGC-GCGUGCUaGC-GCA--UCGUC----AGCA- -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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