miRNA: 3'- gACGGcuucUGGAGUUCGuACUCGca -5'
miRNA: 3'- -GACGGCuucUGGAGUUCGU---------ACUCGCa -5'
miRNA: 3'- gaCGGCUUCugGAGUuc--GUACUCGCa -5'
miRNA: 3'- -GACGGCUUCUGGAGUUCGUACUCGCA- -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 | |||||||
| 15407 | 3' | -53.7 | NC_003907.2 | + | 31368 | 0.66 | 0.742643 |
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Target: 5'- gUGCCa---GCCUCAAGC-UGAGCa- -3' miRNA: 3'- gACGGcuucUGGAGUUCGuACUCGca -5' |
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| 15407 | 3' | -53.7 | NC_003907.2 | + | 27755 | 0.66 | 0.720782 |
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Target: 5'- uCUGCCGu--GCUUCAAGCAggugaugaaUGGGUGa -3' miRNA: 3'- -GACGGCuucUGGAGUUCGU---------ACUCGCa -5' |
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| 15407 | 3' | -53.7 | NC_003907.2 | + | 40279 | 0.66 | 0.709703 |
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Target: 5'- -aGUCGAAGugCUCAccuuCAUGGGUGa -3' miRNA: 3'- gaCGGCUUCugGAGUuc--GUACUCGCa -5' |
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| 15407 | 3' | -53.7 | NC_003907.2 | + | 3436 | 1.09 | 0.00106 |
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Target: 5'- aCUGCCGAAGACCUCAAGCAUGAGCGUg -3' miRNA: 3'- -GACGGCUUCUGGAGUUCGUACUCGCA- -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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