miRNA: 3'- uCGGUc---GACuCC-CGAGG-GUGa----GGGGG- -5'
miRNA: 3'- -UCGGUCGa-------------CUC----CCGa-----GGGUGAGGGGG- -5'
miRNA: 3'- -UCGGUCGACUCc-CGAGG-GUgagGGGG- -5'
miRNA: 3'- -UCGGUCGACUCCCGAGGGUGAGGGGG- -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 | |||||||
| 6018 | 5' | -63 | NC_001809.1 | + | 3383 | 0.67 | 0.069072 |
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Target: 5'- uGCCAcucuCUGuGGuGCUCCuCACggaagCCCCCc -3' miRNA: 3'- uCGGUc---GACuCC-CGAGG-GUGa----GGGGG- -5' |
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| 6018 | 5' | -63 | NC_001809.1 | + | 2373 | 0.67 | 0.063678 |
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Target: 5'- aGGCCAGUgccacucccauuagGAGcuuuGGCaggaacCCCACUCCUCCa -3' miRNA: 3'- -UCGGUCGa-------------CUC----CCGa-----GGGUGAGGGGG- -5' |
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| 6018 | 5' | -63 | NC_001809.1 | + | 8660 | 0.68 | 0.055465 |
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Target: 5'- uGGCCAGCUGAGaaGCUUCaCGa--CCCCa -3' miRNA: 3'- -UCGGUCGACUCc-CGAGG-GUgagGGGG- -5' |
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| 6018 | 5' | -63 | NC_001809.1 | + | 9765 | 1.11 | 0.000009 |
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Target: 5'- aAGCCAGCUGAGGGCUCCCACUCCCCCa -3' miRNA: 3'- -UCGGUCGACUCCCGAGGGUGAGGGGG- -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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