miRNA: 3'- aUAAGGUCg-UUGGCa-UUGUGGG------UGGU- -5'
miRNA: 3'- auAAGGuCGUuGG-CAUUGUGGg---UGGU- -5'
miRNA: 3'- auaaGGUCGUUGGCAUUgug-GGUGgu -5'
miRNA: 3'- -AUAAGGUCGUUGGCAUUGUGGGUGGU- -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 | |||||||
| 15066 | 3' | -51.5 | NC_003739.1 | + | 2262 | 0.66 | 0.241065 |
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Target: 5'- gAUUCCGGaaAACCGgaAACACCCgaagugACCAu -3' miRNA: 3'- aUAAGGUCg-UUGGCa-UUGUGGG------UGGU- -5' |
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| 15066 | 3' | -51.5 | NC_003739.1 | + | 2700 | 0.67 | 0.197958 |
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Target: 5'- -uUUCCcGCAuCCaGUAACACCaucaACCAa -3' miRNA: 3'- auAAGGuCGUuGG-CAUUGUGGg---UGGU- -5' |
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| 15066 | 3' | -51.5 | NC_003739.1 | + | 156 | 0.67 | 0.173088 |
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Target: 5'- ---aCCAGCGGCCGUAGaaaaCCACa- -3' miRNA: 3'- auaaGGUCGUUGGCAUUgug-GGUGgu -5' |
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| 15066 | 3' | -51.5 | NC_003739.1 | + | 2635 | 1.07 | 9.5e-05 |
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Target: 5'- cUAUUCCAGCAACCGUAACACCCACCAu -3' miRNA: 3'- -AUAAGGUCGUUGGCAUUGUGGGUGGU- -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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