miRNA: 3'- -GUCUUUGUUaGGG------------UG-CGA-GACGACGU- -5'
miRNA: 3'- -GUCUu---UGU--UAGGGuGCGAGACG----ACGU- -5'
miRNA: 3'- -GUCUUUGUUA----GGGugCGAGACGa-------CGU- -5'
miRNA: 3'- -GUCUUUGUUAGGGUGCGAGAcGACGU- -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 | |||||||
| 581 | 5' | -51.7 | AC_000015.1 | + | 10756 | 0.66 | 0.761388 |
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Target: 5'- gCAGGGACAG-CCUuuugugauugcuGCuGCUgCUGCUGCGa -3' miRNA: 3'- -GUCUUUGUUaGGG------------UG-CGA-GACGACGU- -5' |
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| 581 | 5' | -51.7 | AC_000015.1 | + | 21463 | 0.67 | 0.693053 |
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Target: 5'- cCAGAccguGCAggGUCCC-CGUUCUGCcgccUGCGg -3' miRNA: 3'- -GUCUu---UGU--UAGGGuGCGAGACG----ACGU- -5' |
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| 581 | 5' | -51.7 | AC_000015.1 | + | 2847 | 0.67 | 0.693053 |
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Target: 5'- uCAGAGACAAUugacUCUugGUUCUGCcagcugugGCAa -3' miRNA: 3'- -GUCUUUGUUA----GGGugCGAGACGa-------CGU- -5' |
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| 581 | 5' | -51.7 | AC_000015.1 | + | 12859 | 0.95 | 0.010997 |
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Target: 5'- uCAGAAACAAUCCCACGCUCU-CUGCAc -3' miRNA: 3'- -GUCUUUGUUAGGGUGCGAGAcGACGU- -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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