miRNA: 3'- gCG---CACuaGC-GUuuCUUGCUGA---AGCC- -5'
miRNA: 3'- gCGCACUAGCGuuucuuGCUGAaGCC- -5'
miRNA: 3'- gCGCACU------AGCGUUucUUGCugAAGCc -5'
miRNA: 3'- -GCGCA-CUAgCGU---UUCUUGCuGAaGCC- -5'
miRNA: 3'- gCGCACuaGCGUuuCUUG------------CUGAAGCC- -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 | |||||||
| 12207 | 5' | -48.7 | NC_003309.1 | + | 44387 | 0.66 | 0.981544 |
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Target: 5'- uGCaaaGUGggCGcCGucGAACGACUgcgUCGGg -3' miRNA: 3'- gCG---CACuaGC-GUuuCUUGCUGA---AGCC- -5' |
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| 12207 | 5' | -48.7 | NC_003309.1 | + | 18726 | 0.67 | 0.967317 |
|
Target: 5'- aGCGUGAUCGUcucgc-CGGCUgCGGc -3' miRNA: 3'- gCGCACUAGCGuuucuuGCUGAaGCC- -5' |
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| 12207 | 5' | -48.7 | NC_003309.1 | + | 33997 | 0.67 | 0.963732 |
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Target: 5'- uGCGUGGcgcaguUCGCGGuaAGCGugUUCGc -3' miRNA: 3'- gCGCACU------AGCGUUucUUGCugAAGCc -5' |
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| 12207 | 5' | -48.7 | NC_003309.1 | + | 37277 | 0.68 | 0.946669 |
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Target: 5'- gCGCGUcGAUgGCGgucGAGGACGuCUaCGGc -3' miRNA: 3'- -GCGCA-CUAgCGU---UUCUUGCuGAaGCC- -5' |
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| 12207 | 5' | -48.7 | NC_003309.1 | + | 5323 | 0.76 | 0.551011 |
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Target: 5'- aGCGUGcgCGCGccGAGCuugcgaacgacgGACUUCGGa -3' miRNA: 3'- gCGCACuaGCGUuuCUUG------------CUGAAGCC- -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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