miRNA: 3'- -GCCCCGGUCGUCGUGUAGACGAUGGC- -5'
miRNA: 3'- gCCC-CGGUCGU-CGUGUAGacgAUGGC- -5'
miRNA: 3'- -GCC-CC-GGUCGUCGUGUAGacgaUGgC- -5'
miRNA: 3'- -GCCCCGGU---------CguCGUGUAG------------ACgAUGGC- -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 | |||||||
| 1092 | 3' | -58.8 | NC_000929.1 | + | 27217 | 1.08 | 0.000273 |
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Target: 5'- gCGGGGCCAGCAGCACAUCUGCUACCGu -3' miRNA: 3'- -GCCCCGGUCGUCGUGUAGACGAUGGC- -5' |
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| 1092 | 3' | -58.8 | NC_000929.1 | + | 13466 | 0.68 | 0.27528 |
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Target: 5'- gGGGuGCCAGCGuGCGCAUCa--UAUCGa -3' miRNA: 3'- gCCC-CGGUCGU-CGUGUAGacgAUGGC- -5' |
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| 1092 | 3' | -58.8 | NC_000929.1 | + | 18377 | 0.67 | 0.328469 |
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Target: 5'- gCGGcGGcCCAGCAGCGCAUCgaugACgGc -3' miRNA: 3'- -GCC-CC-GGUCGUCGUGUAGacgaUGgC- -5' |
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| 1092 | 3' | -58.8 | NC_000929.1 | + | 21098 | 0.67 | 0.328469 |
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Target: 5'- gCGGGGCCAgaaagagacGguGCACAUCcucauuaguccaUG-UGCCGg -3' miRNA: 3'- -GCCCCGGU---------CguCGUGUAG------------ACgAUGGC- -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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