miRNA: 3'- -CACCCgCAGUUGGGgUAUcAGUaGUG- -5'
miRNA: 3'- cACCCGCAGUUGg---------GGUA-----UCAGUa-GUG- -5'
miRNA: 3'- -CACC-CGcAGUUGGGG------UAUCAGUA-GUG- -5'
miRNA: 3'- -CACCCGCAGUUGGGGUAUCAGUAGUG- -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 | |||||||
| 149 | 3' | -53.5 | AC_000006.1 | + | 13391 | 0.66 | 0.653081 |
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Target: 5'- gGUGGG-GUCAACCCgAUA-UCG-CGCa -3' miRNA: 3'- -CACCCgCAGUUGGGgUAUcAGUaGUG- -5' |
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| 149 | 3' | -53.5 | AC_000006.1 | + | 12473 | 0.66 | 0.653081 |
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Target: 5'- uUGGGCGUCAGCaagcugcucaCCGUcgaccGGUCGccCACg -3' miRNA: 3'- cACCCGCAGUUGg---------GGUA-----UCAGUa-GUG- -5' |
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| 149 | 3' | -53.5 | AC_000006.1 | + | 8835 | 0.66 | 0.641472 |
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Target: 5'- cGUGGaGC-UCAACCUCgcgcagGUGGUCAUgCGCg -3' miRNA: 3'- -CACC-CGcAGUUGGGG------UAUCAGUA-GUG- -5' |
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| 149 | 3' | -53.5 | AC_000006.1 | + | 30501 | 1.08 | 0.000814 |
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Target: 5'- gGUGGGCGUCAACCCCAUAGUCAUCACc -3' miRNA: 3'- -CACCCGCAGUUGGGGUAUCAGUAGUG- -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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