miRNA: 3'- -UCCGUAAAUCG-----ACCUAUUGcAGACGU- -5'
miRNA: 3'- uCCGUAAAu--CGACCUAUUGCAGacgu -5'
miRNA: 3'- uCCGu--AAAUCGACCuAUUGCAGA-CGU- -5'
miRNA: 3'- -UCCGUAAAUCGACCUAUUGCAGACGU- -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 | |||||||
| 22834 | 5' | -48.7 | NC_005135.1 | + | 43644 | 0.67 | 0.99757 |
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Target: 5'- cGGGCAUUUGGUuccaaUGGGUGAU-UUUGUAg -3' miRNA: 3'- -UCCGUAAAUCG-----ACCUAUUGcAGACGU- -5' |
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| 22834 | 5' | -48.7 | NC_005135.1 | + | 72260 | 0.7 | 0.981383 |
|
Target: 5'- cGGCAUUUcguGCUGGAUAAUGUUc--- -3' miRNA: 3'- uCCGUAAAu--CGACCUAUUGCAGacgu -5' |
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| 22834 | 5' | -48.7 | NC_005135.1 | + | 61466 | 0.72 | 0.948505 |
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Target: 5'- cGGCccuUUUGGCUGG-UGGCGUUUcGCAa -3' miRNA: 3'- uCCGu--AAAUCGACCuAUUGCAGA-CGU- -5' |
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| 22834 | 5' | -48.7 | NC_005135.1 | + | 64096 | 1.1 | 0.012965 |
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Target: 5'- cAGGCAUUUAGCUGGAUAACGUCUGCAu -3' miRNA: 3'- -UCCGUAAAUCGACCUAUUGCAGACGU- -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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