miRNA: 3'- cCCCU-CGGGa-----------GUGGCCCG----CGC-AGGGU- -5'
miRNA: 3'- -CCCCUCGGGa----GUGGCCCG--CGCAG--GGU- -5'
miRNA: 3'- ccCCUCGGGaGUGGCCCGCGCAGggu -5'
miRNA: 3'- -CCCCUCGGGAGUGGCCCGCGCAGGGU- -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 | |||||||
| 1486 | 5' | -65 | NC_001335.1 | + | 35414 | 0.66 | 0.289471 |
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Target: 5'- cGGGAuGCCCgguucggagcugUACCGGGCcgagGUGuUCCCGg -3' miRNA: 3'- cCCCU-CGGGa-----------GUGGCCCG----CGC-AGGGU- -5' |
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| 1486 | 5' | -65 | NC_001335.1 | + | 9846 | 0.68 | 0.192133 |
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Target: 5'- cGGGGAGCCUgggacCGUCGGGUcgGCGUCgaCCAu -3' miRNA: 3'- -CCCCUCGGGa----GUGGCCCG--CGCAG--GGU- -5' |
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| 1486 | 5' | -65 | NC_001335.1 | + | 41714 | 0.69 | 0.169266 |
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Target: 5'- -cGGAGCCUcCACUGGGUGUGUCg-- -3' miRNA: 3'- ccCCUCGGGaGUGGCCCGCGCAGggu -5' |
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| 1486 | 5' | -65 | NC_001335.1 | + | 22450 | 1.09 | 0.000123 |
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Target: 5'- uGGGGAGCCCUCACCGGGCGCGUCCCAg -3' miRNA: 3'- -CCCCUCGGGAGUGGCCCGCGCAGGGU- -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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