miRNA: 3'- uagGCCGUCCA-CGCCAUuUGcACa-GG- -5'
miRNA: 3'- uagGCCGUcCACGCCAUUugCACAGg -5'
miRNA: 3'- uaGGCCG-----UCCACGCCaUUUGCac--AGG- -5'
miRNA: 3'- -UAGGCCGUCCACGCCAUUUGCACAGG- -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 | |||||||
| 4337 | 3' | -54.8 | NC_001720.1 | + | 17368 | 0.66 | 0.67195 |
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Target: 5'- --gCGGCGGGUaGCGGUGcGCuUGcgCCg -3' miRNA: 3'- uagGCCGUCCA-CGCCAUuUGcACa-GG- -5' |
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| 4337 | 3' | -54.8 | NC_001720.1 | + | 30227 | 0.69 | 0.495108 |
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Target: 5'- --aUGGCA-GUGUGGUGAugGUGUUg -3' miRNA: 3'- uagGCCGUcCACGCCAUUugCACAGg -5' |
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| 4337 | 3' | -54.8 | NC_001720.1 | + | 18017 | 0.7 | 0.443751 |
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Target: 5'- -gCCGGCgccgcGGGUGCGGcGGGCGgcucUCCg -3' miRNA: 3'- uaGGCCG-----UCCACGCCaUUUGCac--AGG- -5' |
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| 4337 | 3' | -54.8 | NC_001720.1 | + | 16314 | 1.11 | 0.000622 |
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Target: 5'- aAUCCGGCAGGUGCGGUAAACGUGUCCg -3' miRNA: 3'- -UAGGCCGUCCACGCCAUUUGCACAGG- -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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