miRNA: 3'- -GCUAACcaaAGGCCCAAAGag--UGGGU- -5'
miRNA: 3'- gCUaaCCAAAGGCCC---AAAGAGUg--GGU- -5'
miRNA: 3'- gcuaaCCAAAGgCCCAA--------AGAG-UGGGU- -5'
miRNA: 3'- -GCUaaCCAaa-GGCCCA------------AAGAGUGGGU- -5'
miRNA: 3'- -GCUAACCAAAGGCCCAAAGAGUGGGU- -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 | |||||||
| 10411 | 5' | -50.6 | NC_002687.1 | + | 115470 | 0.66 | 0.999853 |
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Target: 5'- uCGAUUGuc-UCCGGGUUUCgcagACUCAc -3' miRNA: 3'- -GCUAACcaaAGGCCCAAAGag--UGGGU- -5' |
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| 10411 | 5' | -50.6 | NC_002687.1 | + | 311995 | 0.68 | 0.998785 |
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Target: 5'- aGAgaGGUUUUCGGGcauUUUCUCGacaCCAc -3' miRNA: 3'- gCUaaCCAAAGGCCC---AAAGAGUg--GGU- -5' |
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| 10411 | 5' | -50.6 | NC_002687.1 | + | 157553 | 0.68 | 0.997567 |
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Target: 5'- ----cGGUUUCgGGGUUcauccacuUCUCuGCCCAg -3' miRNA: 3'- gcuaaCCAAAGgCCCAA--------AGAG-UGGGU- -5' |
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| 10411 | 5' | -50.6 | NC_002687.1 | + | 145096 | 0.72 | 0.969339 |
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Target: 5'- aCGAa-GGUacgCCGGGUuuggacauauacUUCUCACCCAg -3' miRNA: 3'- -GCUaaCCAaa-GGCCCA------------AAGAGUGGGU- -5' |
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| 10411 | 5' | -50.6 | NC_002687.1 | + | 293149 | 1.09 | 0.021405 |
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Target: 5'- gCGAUUGGUUUCCGGGUUUCUCACCCAc -3' miRNA: 3'- -GCUAACCAAAGGCCCAAAGAGUGGGU- -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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