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miRNA: 3'- -UGAC-AGGaUCUCUGGUAgGCGUGUaa -5'
miRNA: 3'- -UGACAG-GAUCUCUGgU-----AGGCGUGuaa -5'
miRNA: 3'- -UGA--CAGGA--------------UCUCUGGUAGGCGUGuaa -5'
miRNA: 3'- -UGACAGGAUCUCUGGUAGGCGUGUAA- -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#
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P value |
| Predicted miRNA align pattern | |||||||
| 16644 | 3' | -53 | NC_004156.1 | + | 203807 | 0.66 | 0.984068 |
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Target: 5'- uGCUGuUCCcAGGGAUCAU-CGCACGg- -3' miRNA: 3'- -UGAC-AGGaUCUCUGGUAgGCGUGUaa -5' |
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| 16644 | 3' | -53 | NC_004156.1 | + | 78847 | 0.69 | 0.933786 |
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Target: 5'- aGCUGUCgCUGGAGACgGugcucUCUGCGCu-- -3' miRNA: 3'- -UGACAG-GAUCUCUGgU-----AGGCGUGuaa -5' |
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| 16644 | 3' | -53 | NC_004156.1 | + | 26252 | 0.7 | 0.915774 |
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Target: 5'- cGCUcgGUUCUuaucgcaacagaguGGGGGCCAUCCGCACu-- -3' miRNA: 3'- -UGA--CAGGA--------------UCUCUGGUAGGCGUGuaa -5' |
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| 16644 | 3' | -53 | NC_004156.1 | + | 101914 | 1.05 | 0.013262 |
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Target: 5'- aACUGUCCUAGAGACCAUCCGCACAUUu -3' miRNA: 3'- -UGACAGGAUCUCUGGUAGGCGUGUAA- -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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