miRNA: 3'- gCC-GACGc---UG-CCCCgGGAGGUCCCCc -5'
miRNA: 3'- gCCGACG------CUGCCC-CGGGAg-GUCCc-CC- -5'
miRNA: 3'- -GCCGACGCUGCCCCGGGAGGUCCCCC- -5'
Results 1 - 3 of 3 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 | |||||||
| 2455 | 3' | -66.1 | NC_001436.1 | + | 967 | 0.67 | 0.03915 |
|
Target: 5'- uGGuCUGCauaaACuGGGGgCUUCCAGGGGc -3' miRNA: 3'- gCC-GACGc---UG-CCCCgGGAGGUCCCCc -5' |
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| 2455 | 3' | -66.1 | NC_001436.1 | + | 7634 | 0.67 | 0.037945 |
|
Target: 5'- aGGCUGUcagcguGACGGGuGCCCUagCAGGcuGGa -3' miRNA: 3'- gCCGACG------CUGCCC-CGGGAg-GUCCc-CC- -5' |
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| 2455 | 3' | -66.1 | NC_001436.1 | + | 6763 | 1.1 | 0.000005 |
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Target: 5'- cCGGCUGCGACGGGGCCCUCCAGGGGGg -3' miRNA: 3'- -GCCGACGCUGCCCCGGGAGGUCCCCC- -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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