miRNA: 3'- -ACCCCCCGAUGAUGUGUAGGCAGUCG- -5'
miRNA: 3'- -ACCC----------CCCGAUGaUGUGUAGgcaGUCG- -5'
miRNA: 3'- accCCCCGAUGa-UGUGU------------AGGCa--GUCG- -5'
miRNA: 3'- aCCCCCC-Ga------UGAUGUgUa---GGCa---GUCG- -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 |
| Predicted miRNA align pattern | |||||||
| 15349 | 5' | -55.7 | NC_003876.1 | + | 4528 | 1.12 | 1.2e-05 |
|
Target: 5'- cUGGGGGGCUACUACACAUCCGUCAGCa -3' miRNA: 3'- -ACCCCCCGAUGAUGUGUAGGCAGUCG- -5' |
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| 15349 | 5' | -55.7 | NC_003876.1 | + | 1418 | 0.66 | 0.125299 |
|
Target: 5'- cUGGGuacacucuucGGGCUGC-ACACAUCaagCGGUg -3' miRNA: 3'- -ACCC----------CCCGAUGaUGUGUAGgcaGUCG- -5' |
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| 15349 | 5' | -55.7 | NC_003876.1 | + | 4365 | 0.66 | 0.125299 |
|
Target: 5'- --cGGGGCUGCgcGCACAcucgugaaccgaUCCGgcgCAGUa -3' miRNA: 3'- accCCCCGAUGa-UGUGU------------AGGCa--GUCG- -5' |
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| 15349 | 5' | -55.7 | NC_003876.1 | + | 2506 | 0.66 | 0.113246 |
|
Target: 5'- cGGGGGGaCguugggaGCUGCAgGgccgCCGguagCGGCu -3' miRNA: 3'- aCCCCCC-Ga------UGAUGUgUa---GGCa---GUCG- -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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