miRNA: 3'- gGCGUUGGGC-CGcAAG----AGUAGCGCGu -5'
miRNA: 3'- -GGCGuUGG----------GCC-GCAAGAGUAGCGCgu -5'
miRNA: 3'- -GGCGuUGGG--CCGCA---AGAGua------GCGCGU- -5'
miRNA: 3'- -GGCGUUGGGCCgcaaGagua-GCGCGU- -5'
Results 21 - 24 of 24 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 | |||||||
| 8098 | 3' | -56.6 | NC_001978.2 | + | 15027 | 0.66 | 0.580043 |
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Target: 5'- gCGCAAUCUGuGC-UUCggcuUCGUCGCGCc -3' miRNA: 3'- gGCGUUGGGC-CGcAAG----AGUAGCGCGu -5' |
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| 8098 | 3' | -56.6 | NC_001978.2 | + | 10345 | 0.66 | 0.591011 |
|
Target: 5'- aUCGCuGCCauugucggguUGGuCGUUCUCAUCGUGg- -3' miRNA: 3'- -GGCGuUGG----------GCC-GCAAGAGUAGCGCgu -5' |
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| 8098 | 3' | -56.6 | NC_001978.2 | + | 26356 | 0.66 | 0.591011 |
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Target: 5'- gCCGC-GCCCauGGCGUgaaUCUCcugacgcaCGCGCGu -3' miRNA: 3'- -GGCGuUGGG--CCGCA---AGAGua------GCGCGU- -5' |
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| 8098 | 3' | -56.6 | NC_001978.2 | + | 31417 | 0.66 | 0.602014 |
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Target: 5'- gCCGCAACCCGGgacgCgaaagCGUGCAc -3' miRNA: 3'- -GGCGUUGGGCCgcaaGagua-GCGCGU- -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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