miRNA: 3'- guUG-GGUUCGUGGGGG---------AGUACGaacc -5'
miRNA: 3'- -GUuGGGUUCGUGG-----------GGGAGU--ACGAacc -5'
miRNA: 3'- gUUGGgu--UCGUGGG--GGAGU---ACGAACc -5'
miRNA: 3'- guuGGGUUCGUG-GGGGAGuacGAACC- -5'
miRNA: 3'- -GUUGGGUUCGUGGGGGAGUACGAACC- -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 | |||||||
| 8841 | 3' | -54.6 | NC_002484.1 | + | 35784 | 0.66 | 0.718113 |
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Target: 5'- -cGCgCCAAGCGCUCCCaggagugaaUCAUGCa--- -3' miRNA: 3'- guUG-GGUUCGUGGGGG---------AGUACGaacc -5' |
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| 8841 | 3' | -54.6 | NC_002484.1 | + | 33325 | 0.66 | 0.718113 |
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Target: 5'- cCAcCCCAGGCACUccguugacuggCCCUCAauUGCUg-- -3' miRNA: 3'- -GUuGGGUUCGUGG-----------GGGAGU--ACGAacc -5' |
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| 8841 | 3' | -54.6 | NC_002484.1 | + | 7619 | 0.67 | 0.674427 |
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Target: 5'- uGGCCaauuGGCGCCCauCCUCAagcUGCUUGc -3' miRNA: 3'- gUUGGgu--UCGUGGG--GGAGU---ACGAACc -5' |
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| 8841 | 3' | -54.6 | NC_002484.1 | + | 9485 | 0.69 | 0.563806 |
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Target: 5'- --gUCCGAGCGCuCCCCUUu--CUUGGg -3' miRNA: 3'- guuGGGUUCGUG-GGGGAGuacGAACC- -5' |
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| 8841 | 3' | -54.6 | NC_002484.1 | + | 30891 | 1.11 | 0.000775 |
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Target: 5'- aCAACCCAAGCACCCCCUCAUGCUUGGa -3' miRNA: 3'- -GUUGGGUUCGUGGGGGAGUACGAACC- -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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