miRNA: 3'- -CCG--UACGAUugGGUGGUGauGAUGUC- -5'
miRNA: 3'- -CCG--UACGAUUGGGUGG-UGAUGau-GUc -5'
miRNA: 3'- ccGUACGAUUG-GGUGGUGAUGa-------------UGUC- -5'
miRNA: 3'- -CCGUACGAUUGGGUGGUGAUGAUGUC- -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 | |||||||
| 18039 | 3' | -50.5 | NC_004667.1 | + | 4432 | 0.66 | 0.622666 |
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Target: 5'- cGGUuuGUGCUGugUUACCAU--CUGCAGc -3' miRNA: 3'- -CCG--UACGAUugGGUGGUGauGAUGUC- -5' |
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| 18039 | 3' | -50.5 | NC_004667.1 | + | 14735 | 0.72 | 0.314772 |
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Target: 5'- uGGUcuGUGCUAACCCAUCgACUACguuCAc -3' miRNA: 3'- -CCG--UACGAUUGGGUGG-UGAUGau-GUc -5' |
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| 18039 | 3' | -50.5 | NC_004667.1 | + | 7886 | 0.72 | 0.300989 |
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Target: 5'- -aCGUGUUAGCaCCACCACUGCgccucugagagccgACAGa -3' miRNA: 3'- ccGUACGAUUG-GGUGGUGAUGa-------------UGUC- -5' |
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| 18039 | 3' | -50.5 | NC_004667.1 | + | 9409 | 1.13 | 0.000356 |
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Target: 5'- uGGCAUGCUAACCCACCACUACUACAGg -3' miRNA: 3'- -CCGUACGAUUGGGUGGUGAUGAUGUC- -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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