miRNA: 3'- gGACCACGCCGAGcCGUaucucguac -5'
miRNA: 3'- ggaCCACGCCG----AGCCGuauCUCGUAc -5'
miRNA: 3'- -GGaCCa-CGCCGAGCCGua------UCUCGUAC- -5'
miRNA: 3'- -GGACCA-CGCCGAgCCGUau-----CUCgUAC- -5'
miRNA: 3'- -GGACCACGCCGAGCCGUAUCUCGUAC- -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 | |||||||
| 30447 | 3' | -56.2 | NC_006548.1 | + | 36791 | 0.66 | 0.547847 |
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Target: 5'- gCUGGUGCGGCUCaGCAg-------- -3' miRNA: 3'- gGACCACGCCGAGcCGUaucucguac -5' |
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| 30447 | 3' | -56.2 | NC_006548.1 | + | 1263 | 0.68 | 0.432407 |
|
Target: 5'- --cGGUGCGGCaggcUUGGCuuuGAGCGUc -3' miRNA: 3'- ggaCCACGCCG----AGCCGuauCUCGUAc -5' |
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| 30447 | 3' | -56.2 | NC_006548.1 | + | 1960 | 0.68 | 0.42261 |
|
Target: 5'- aCCaGGccGUGGCUCGGCuuacucagGGGGUGUGa -3' miRNA: 3'- -GGaCCa-CGCCGAGCCGua------UCUCGUAC- -5' |
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| 30447 | 3' | -56.2 | NC_006548.1 | + | 30242 | 0.71 | 0.271046 |
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Target: 5'- aCCUGGUcGCGGCUgGGCAggccuacGAG-AUGg -3' miRNA: 3'- -GGACCA-CGCCGAgCCGUau-----CUCgUAC- -5' |
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| 30447 | 3' | -56.2 | NC_006548.1 | + | 20140 | 1.1 | 0.000418 |
|
Target: 5'- aCCUGGUGCGGCUCGGCAUAGAGCAUGc -3' miRNA: 3'- -GGACCACGCCGAGCCGUAUCUCGUAC- -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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