miRNA: 3'- auGUUGUCGGACGacucaCCAGGACU- -5'
miRNA: 3'- aUGUUGUCGGA--------CGAC----UCACC--------AGGACU- -5'
miRNA: 3'- -AUGUUGUCGGa---CGACUCaCCa---GGACU- -5'
miRNA: 3'- -AUGUUGUCGGACGACUCACCAGGACU- -5'
Results 1 - 4 of 4 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 | |||||||
| 13013 | 5' | -54.6 | NC_003390.1 | + | 41372 | 0.66 | 0.64385 |
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Target: 5'- -cCAGCAGCCUGCa----GGUCUUGGa -3' miRNA: 3'- auGUUGUCGGACGacucaCCAGGACU- -5' |
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| 13013 | 5' | -54.6 | NC_003390.1 | + | 20256 | 0.71 | 0.387754 |
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Target: 5'- cACAGCAGCCUggauguugGCUGggagGGUGGcauggagcUCCUGAg -3' miRNA: 3'- aUGUUGUCGGA--------CGAC----UCACC--------AGGACU- -5' |
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| 13013 | 5' | -54.6 | NC_003390.1 | + | 30928 | 0.72 | 0.33459 |
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Target: 5'- cUGCAGCAGCCggugGCUGAG-GGcugaCUUGAg -3' miRNA: 3'- -AUGUUGUCGGa---CGACUCaCCa---GGACU- -5' |
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| 13013 | 5' | -54.6 | NC_003390.1 | + | 4881 | 1.08 | 0.000936 |
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Target: 5'- gUACAACAGCCUGCUGAGUGGUCCUGAg -3' miRNA: 3'- -AUGUUGUCGGACGACUCACCAGGACU- -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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