miRNA: 3'- gAGG-AGU------------GUGGGUAGGACCUUA--CGCA- -5'
miRNA: 3'- gAGGa----GUG---UGG-GUA-GGACCuuACGCA- -5'
miRNA: 3'- gaGGAGu--GUGGGuaGGACCUUAC-GCA- -5'
miRNA: 3'- -GAGGAGUGUGGGUAGGACCUUACGCA- -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 | |||||||
| 13242 | 5' | -54.7 | NC_003401.1 | + | 79823 | 0.67 | 0.881747 |
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Target: 5'- gUCCuUCAagcacagacuuuUACCCAUUCUGGGAUggGCGUu -3' miRNA: 3'- gAGG-AGU------------GUGGGUAGGACCUUA--CGCA- -5' |
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| 13242 | 5' | -54.7 | NC_003401.1 | + | 122824 | 0.68 | 0.859181 |
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Target: 5'- gUCCccgugCACucuACCgCGUcCCUGGggUGCGUg -3' miRNA: 3'- gAGGa----GUG---UGG-GUA-GGACCuuACGCA- -5' |
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| 13242 | 5' | -54.7 | NC_003401.1 | + | 45079 | 0.68 | 0.851222 |
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Target: 5'- -aCCUCuguCGCCCcaCCUGGAAUGaUGUa -3' miRNA: 3'- gaGGAGu--GUGGGuaGGACCUUAC-GCA- -5' |
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| 13242 | 5' | -54.7 | NC_003401.1 | + | 105867 | 1.07 | 0.004316 |
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Target: 5'- gCUCCUCACACCCAUCCUGGAAUGCGUc -3' miRNA: 3'- -GAGGAGUGUGGGUAGGACCUUACGCA- -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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