miRNA: 3'- -GCUGAC-CCGuuCCCACCuuACAGGGU- -5'
miRNA: 3'- -GCUGaCCCGUUCCCaccUUACAGGGU- -5'
miRNA: 3'- gCUGA--CCCGU------UCCCACCU----UACAGGGU- -5'
miRNA: 3'- -GCUG---------ACCCGu--UCC-CACCUUACAGGGu -5'
miRNA: 3'- -GCUGACCCGUUCCCACCUUACAGGGU- -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 | |||||||
| 18224 | 3' | -56.1 | NC_004680.1 | + | 45564 | 0.67 | 0.603414 |
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Target: 5'- aCGAUUGaGGUgcGGGUGG--UGUUCCGc -3' miRNA: 3'- -GCUGAC-CCGuuCCCACCuuACAGGGU- -5' |
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| 18224 | 3' | -56.1 | NC_004680.1 | + | 56622 | 0.7 | 0.41833 |
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Target: 5'- aCGGCaGGGCGAGGGc--GAUGUCUCGg -3' miRNA: 3'- -GCUGaCCCGUUCCCaccUUACAGGGU- -5' |
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| 18224 | 3' | -56.1 | NC_004680.1 | + | 56878 | 0.72 | 0.347699 |
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Target: 5'- aGGCUgaGGGCGugcugcAGGGUGGAggucAUGUCUCGc -3' miRNA: 3'- gCUGA--CCCGU------UCCCACCU----UACAGGGU- -5' |
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| 18224 | 3' | -56.1 | NC_004680.1 | + | 13794 | 0.73 | 0.308079 |
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Target: 5'- uCGAUggugcuuggUGGGUuucAGGaGUGGAGUGUCCCu -3' miRNA: 3'- -GCUG---------ACCCGu--UCC-CACCUUACAGGGu -5' |
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| 18224 | 3' | -56.1 | NC_004680.1 | + | 46451 | 1.09 | 0.000912 |
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Target: 5'- aCGACUGGGCAAGGGUGGAAUGUCCCAc -3' miRNA: 3'- -GCUGACCCGUUCCCACCUUACAGGGU- -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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