miRNA: 3'- cCGACUCaaGCUGacc---CAGUGGCGGc -5'
miRNA: 3'- -CCG---ACUCa---------AGCUGa--CC-CAGUGGCGGC- -5'
miRNA: 3'- -CCGACUcaa-GCUGACCCa---GUGGCGGC- -5'
miRNA: 3'- -CCGACUCAAGCUGACCCAGUGGCGGC- -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 | |||||||
| 12692 | 5' | -57 | NC_003347.1 | + | 2566 | 0.68 | 0.112592 |
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Target: 5'- cGCUGAGccCGACgcccccGUCACCGCCc -3' miRNA: 3'- cCGACUCaaGCUGacc---CAGUGGCGGc -5' |
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| 12692 | 5' | -57 | NC_003347.1 | + | 5649 | 0.68 | 0.109032 |
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Target: 5'- gGGUucaUGGGggggacgcggUCGACgagGGaGUCAUCGCCGg -3' miRNA: 3'- -CCG---ACUCa---------AGCUGa--CC-CAGUGGCGGC- -5' |
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| 12692 | 5' | -57 | NC_003347.1 | + | 651 | 0.77 | 0.02148 |
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Target: 5'- gGGUUGGaaggCGGCUGGGggggCGCCGCCGu -3' miRNA: 3'- -CCGACUcaa-GCUGACCCa---GUGGCGGC- -5' |
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| 12692 | 5' | -57 | NC_003347.1 | + | 1612 | 1.11 | 0.000025 |
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Target: 5'- aGGCUGAGUUCGACUGGGUCACCGCCGa -3' miRNA: 3'- -CCGACUCAAGCUGACCCAGUGGCGGC- -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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