miRNA: 3'- uaUAGGUGGCAGaCGUG----CGgUUCaGG- -5'
miRNA: 3'- uauaGGUGGCaGACG--------------UG-CGGUUCAGg -5'
miRNA: 3'- -UAUaGGUGGCaga-----CGUGCGGU--UCAGG- -5'
miRNA: 3'- -UAUAGGuGGCAG-ACGUGCGGuUCaGG- -5'
miRNA: 3'- -UAUAGGUGGCAGACGUGCGGUUCAGG- -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 | |||||||
| 2511 | 5' | -53.7 | NC_001454.1 | + | 16052 | 0.66 | 0.668627 |
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Target: 5'- -cGUCCACCGUUaGCACugcgGUgGAGgCCa -3' miRNA: 3'- uaUAGGUGGCAGaCGUG----CGgUUCaGG- -5' |
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| 2511 | 5' | -53.7 | NC_001454.1 | + | 33064 | 0.66 | 0.665166 |
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Target: 5'- ---cCCACCG-CUGCguuggugaaaaauuACaGCCAAGUCa -3' miRNA: 3'- uauaGGUGGCaGACG--------------UG-CGGUUCAGg -5' |
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| 2511 | 5' | -53.7 | NC_001454.1 | + | 13245 | 0.66 | 0.622328 |
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Target: 5'- aGUG-CCGCCGgugauggcGUACGCCGagGGUCCu -3' miRNA: 3'- -UAUaGGUGGCaga-----CGUGCGGU--UCAGG- -5' |
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| 2511 | 5' | -53.7 | NC_001454.1 | + | 24943 | 0.7 | 0.394957 |
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Target: 5'- aGUAUCC-CCGUCgUGCGCGCUuAGgCUg -3' miRNA: 3'- -UAUAGGuGGCAG-ACGUGCGGuUCaGG- -5' |
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| 2511 | 5' | -53.7 | NC_001454.1 | + | 16063 | 1.11 | 0.000506 |
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Target: 5'- gAUAUCCACCGUCUGCACGCCAAGUCCg -3' miRNA: 3'- -UAUAGGUGGCAGACGUGCGGUUCAGG- -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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