miRNA: 3'- -CCGAUGAGGa----------CUGACaguAAC-GCUGc -5'
miRNA: 3'- ccGAUGAGGAc---UGACAGUaaCGCUGC- -5'
miRNA: 3'- cCGAUGa----GGACUGACaguaaCGCUGC- -5'
miRNA: 3'- -CCGAUGaGGACUGACa--GU---AACGCUGc -5'
miRNA: 3'- -CCGAUGAGGACUGACAGUAACGCUGC- -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 | |||||||
| 31890 | 3' | -51.3 | NC_006938.1 | + | 50200 | 0.67 | 0.886551 |
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Target: 5'- cGGCUACUCCgcccaggcaccGGCUGgcuUUGuCGACa -3' miRNA: 3'- -CCGAUGAGGa----------CUGACaguAAC-GCUGc -5' |
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| 31890 | 3' | -51.3 | NC_006938.1 | + | 60316 | 0.69 | 0.789545 |
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Target: 5'- -cCUAUUCCUuggaACUGUCAgcGCGGCGg -3' miRNA: 3'- ccGAUGAGGAc---UGACAGUaaCGCUGC- -5' |
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| 31890 | 3' | -51.3 | NC_006938.1 | + | 56851 | 0.71 | 0.672413 |
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Target: 5'- uGCUGCcaccgCCUGACUGg----GCGACGa -3' miRNA: 3'- cCGAUGa----GGACUGACaguaaCGCUGC- -5' |
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| 31890 | 3' | -51.3 | NC_006938.1 | + | 31802 | 0.75 | 0.475939 |
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Target: 5'- cGGCUGC-CCUGGCUGacgCGcccUUGCGGCc -3' miRNA: 3'- -CCGAUGaGGACUGACa--GU---AACGCUGc -5' |
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| 31890 | 3' | -51.3 | NC_006938.1 | + | 51212 | 1.13 | 0.001842 |
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Target: 5'- gGGCUACUCCUGACUGUCAUUGCGACGg -3' miRNA: 3'- -CCGAUGAGGACUGACAGUAACGCUGC- -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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