miRNA: 3'- -GGCCUUUGGCCAcucuaAUGACGccu -5'
miRNA: 3'- -GGCCuuUGGCCaCUCUAa---UGACgCCU- -5'
miRNA: 3'- gGCCUUuGGCCaCUCUaauGACGCCU- -5'
miRNA: 3'- gGCCUuuGGCCACUCUAa---UG--ACGCCU- -5'
miRNA: 3'- -GGCCUU-------------UGGCCACUCUaaUgaCGCCu -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 | |||||||
| 30905 | 3' | -51.5 | NC_006552.1 | + | 2948 | 0.69 | 0.798664 |
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Target: 5'- aCCGGAGACCGGUug---UGCUGCc-- -3' miRNA: 3'- -GGCCUUUGGCCAcucuaAUGACGccu -5' |
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| 30905 | 3' | -51.5 | NC_006552.1 | + | 59631 | 0.69 | 0.798664 |
|
Target: 5'- cUCGG--GCCGG-GAGGUgcugGCUGgGGAc -3' miRNA: 3'- -GGCCuuUGGCCaCUCUAa---UGACgCCU- -5' |
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| 30905 | 3' | -51.5 | NC_006552.1 | + | 12805 | 0.69 | 0.798664 |
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Target: 5'- gCGGAAcUCGGcGAGGgu-CUGCGGGu -3' miRNA: 3'- gGCCUUuGGCCaCUCUaauGACGCCU- -5' |
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| 30905 | 3' | -51.5 | NC_006552.1 | + | 27065 | 0.7 | 0.748297 |
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Target: 5'- uUGGAc-CCGGUGGGGUgaagACguUGCGGAc -3' miRNA: 3'- gGCCUuuGGCCACUCUAa---UG--ACGCCU- -5' |
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| 30905 | 3' | -51.5 | NC_006552.1 | + | 11721 | 0.73 | 0.616928 |
|
Target: 5'- aCCGGAAgcacgauggccuuGCCGGUGAGGccGgaGCGGc -3' miRNA: 3'- -GGCCUU-------------UGGCCACUCUaaUgaCGCCu -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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