miRNA: 3'- -AAGgAGGUGCAu-----CUCGC-CCAGuuGGa -5'
miRNA: 3'- -AAGGa---GGu---GCAUCUCGcCCAGUUGGa -5'
miRNA: 3'- aaGGAGGUGCaUCUCGCC-------------CAGu--UGGa -5'
miRNA: 3'- aaGGAGGUGCaUCUCGCCCaGU---UGGA- -5'
miRNA: 3'- -AAGGAGGUGCAUCUCGCCCAGUUGGA- -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 | |||||||
| 22059 | 5' | -56.2 | NC_004927.1 | + | 27549 | 0.67 | 0.675689 |
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Target: 5'- uUUCgUCCACGUccauucGAGCGuGGUCggUCa -3' miRNA: 3'- -AAGgAGGUGCAu-----CUCGC-CCAGuuGGa -5' |
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| 22059 | 5' | -56.2 | NC_004927.1 | + | 67534 | 0.68 | 0.610885 |
|
Target: 5'- gUUCCgcgaCCuguuCGUGGAGCaGGUUGACCa -3' miRNA: 3'- -AAGGa---GGu---GCAUCUCGcCCAGUUGGa -5' |
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| 22059 | 5' | -56.2 | NC_004927.1 | + | 12461 | 0.68 | 0.599015 |
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Target: 5'- -aCCUCCACG-AGAGCGGaguuucggguaacGUCcuuGCCg -3' miRNA: 3'- aaGGAGGUGCaUCUCGCC-------------CAGu--UGGa -5' |
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| 22059 | 5' | -56.2 | NC_004927.1 | + | 43109 | 0.72 | 0.363938 |
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Target: 5'- -aCCUCCACGgGGAGCGGGaCAggaAUCUu -3' miRNA: 3'- aaGGAGGUGCaUCUCGCCCaGU---UGGA- -5' |
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| 22059 | 5' | -56.2 | NC_004927.1 | + | 33328 | 1.05 | 0.00214 |
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Target: 5'- gUUCCUCCACGUAGAGCGGGUCAACCUu -3' miRNA: 3'- -AAGGAGGUGCAUCUCGCCCAGUUGGA- -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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