miRNA: 3'- aaUGUGUAGCCgCAUUg-GUAGGGCUA- -5'
miRNA: 3'- -AAUGUGUAgCCGCAUUGGu--AgGGCUa -5'
miRNA: 3'- aaugUGUAG---CCGCA----UUGGUAGGGCUa -5'
miRNA: 3'- aAUGuGUAGCCGCAu-UGGU--AGGGCUa -5'
miRNA: 3'- -AAUGUGUAGCCGCAUUGGUAGGGCUA- -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 | |||||||
| 31923 | 5' | -52.3 | NC_006940.1 | + | 23273 | 0.66 | 0.759035 |
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Target: 5'- -gGCGCGUCGGaGUGGgaCAUCUCGGUu -3' miRNA: 3'- aaUGUGUAGCCgCAUUg-GUAGGGCUA- -5' |
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| 31923 | 5' | -52.3 | NC_006940.1 | + | 32413 | 0.68 | 0.621864 |
|
Target: 5'- aUUACGCAU-GGCGUGGCCcccUgCCGAa -3' miRNA: 3'- -AAUGUGUAgCCGCAUUGGu--AgGGCUa -5' |
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| 31923 | 5' | -52.3 | NC_006940.1 | + | 38063 | 0.69 | 0.541054 |
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Target: 5'- ---aGCGUUuagGGCGUcuccAACCAUCCCGAa -3' miRNA: 3'- aaugUGUAG---CCGCA----UUGGUAGGGCUa -5' |
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| 31923 | 5' | -52.3 | NC_006940.1 | + | 23156 | 0.7 | 0.529755 |
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Target: 5'- aUGCuCAUCGGUGUuuGCCAguUCCUGAa -3' miRNA: 3'- aAUGuGUAGCCGCAu-UGGU--AGGGCUa -5' |
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| 31923 | 5' | -52.3 | NC_006940.1 | + | 12150 | 1.03 | 0.002922 |
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Target: 5'- aUUACACAUCGGCGUAACCAUCCCGAUu -3' miRNA: 3'- -AAUGUGUAGCCGCAUUGGUAGGGCUA- -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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