miRNA: 3'- gGUGGUCUu---UGU--CGaCCCGCCa----GUCU- -5'
miRNA: 3'- gGUGGUCUUUG----UCGACCC-GCCagucu -5'
miRNA: 3'- gGUGGUCuuUGUCGA---C-CCGCC-AGUCU- -5'
miRNA: 3'- -GGUGGUCUUUGUCGACCCGCCAGUCU- -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 | |||||||
| 708 | 5' | -54.9 | AC_000019.1 | + | 11846 | 0.66 | 0.609176 |
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Target: 5'- gCACCGGAucccGCAauGC-GGGCGGcgcugCAGAg -3' miRNA: 3'- gGUGGUCUu---UGU--CGaCCCGCCa----GUCU- -5' |
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| 708 | 5' | -54.9 | AC_000019.1 | + | 14337 | 0.68 | 0.497895 |
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Target: 5'- aCACCAGGAACuucaAGCUGGGaUGGg---- -3' miRNA: 3'- gGUGGUCUUUG----UCGACCC-GCCagucu -5' |
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| 708 | 5' | -54.9 | AC_000019.1 | + | 17256 | 0.68 | 0.497895 |
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Target: 5'- aUACCAGgcAUAGCUuccGuGGCGGuUCAGGc -3' miRNA: 3'- gGUGGUCuuUGUCGA---C-CCGCC-AGUCU- -5' |
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| 708 | 5' | -54.9 | AC_000019.1 | + | 11286 | 1.12 | 0.00039 |
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Target: 5'- aCCACCAGAAACAGCUGGGCGGUCAGAg -3' miRNA: 3'- -GGUGGUCUUUGUCGACCCGCCAGUCU- -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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