miRNA: 3'- -UACU----UGGCAGUAGCU--CGGGCCCagaa -5'
miRNA: 3'- -UACuu--GGCaGU---AGCUCGGGCCCAGaa -5'
miRNA: 3'- -UACUUGGCAGUAGCUCGGGCCCAGAA- -5'
Results 1 - 3 of 3 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 | |||||||
| 16580 | 5' | -56.7 | NC_004117.1 | + | 29029 | 0.66 | 0.871015 |
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Target: 5'- uGUGAaaccAUCGUUGUCGAcgGCCCGGGg--- -3' miRNA: 3'- -UACU----UGGCAGUAGCU--CGGGCCCagaa -5' |
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| 16580 | 5' | -56.7 | NC_004117.1 | + | 142761 | 0.69 | 0.689808 |
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Target: 5'- cGUGuaauCCG-CAuauUCGAGCCCGGGUUa- -3' miRNA: 3'- -UACuu--GGCaGU---AGCUCGGGCCCAGaa -5' |
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| 16580 | 5' | -56.7 | NC_004117.1 | + | 18265 | 1.04 | 0.004995 |
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Target: 5'- aAUGAACCGUCAUCGAGCCCGGGUCUUa -3' miRNA: 3'- -UACUUGGCAGUAGCUCGGGCCCAGAA- -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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