miRNA: 3'- aUGUCGUGCGGGGa----GGCGGgggUCGa -5'
miRNA: 3'- aUGU--CGuGCGGGGAGGCGG-------GGGUCga -5'
miRNA: 3'- aUGU---CGUgCGGGGaGGC---GGGGGUCGa -5'
miRNA: 3'- aUGUCGu------------GCGGGGAGGCGGGGGuCGa -5'
miRNA: 3'- auGUCGUgCGGGGag--GCGGGGGUCga -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 | |||||||
| 30663 | 5' | -64.6 | NC_006549.1 | + | 7772 | 0.66 | 0.44492 |
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Target: 5'- gGCAGCGCGUCCUcggggCCGCCa--GGCg -3' miRNA: 3'- aUGUCGUGCGGGGa----GGCGGgggUCGa -5' |
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| 30663 | 5' | -64.6 | NC_006549.1 | + | 77179 | 0.67 | 0.409764 |
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Target: 5'- gGCAucGCcCGCCCUUCCGCCaaaaccuCCCAGg- -3' miRNA: 3'- aUGU--CGuGCGGGGAGGCGG-------GGGUCga -5' |
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| 30663 | 5' | -64.6 | NC_006549.1 | + | 41718 | 0.68 | 0.370095 |
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Target: 5'- gGCGcccGCGgGCCCC-CCGgccCCCCCGGCc -3' miRNA: 3'- aUGU---CGUgCGGGGaGGC---GGGGGUCGa -5' |
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| 30663 | 5' | -64.6 | NC_006549.1 | + | 37839 | 0.69 | 0.315344 |
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Target: 5'- cGCAGCcgccuccgccuccCGCUCCUCCGCCUCC-GCc -3' miRNA: 3'- aUGUCGu------------GCGGGGAGGCGGGGGuCGa -5' |
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| 30663 | 5' | -64.6 | NC_006549.1 | + | 79369 | 0.69 | 0.297614 |
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Target: 5'- -uCAGCA-GCCCCcagaCGCCCCCAGa- -3' miRNA: 3'- auGUCGUgCGGGGag--GCGGGGGUCga -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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