miRNA: 3'- -UGUa--UCGCCaa--CCGCCAU--UCGUGuaG- -5'
miRNA: 3'- -UGUA----UCGCCaa--CCGCCAUU-CGU-GUAG- -5'
miRNA: 3'- ugUAUCGc--CAACCGCCA--UUCG-------------UGUAG- -5'
miRNA: 3'- -UGUAUCGCCAACCGCCAUUCGUGUAG- -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 | |||||||
| 27505 | 3' | -51.6 | NC_005879.1 | + | 11306 | 0.66 | 0.778072 |
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Target: 5'- aGCAggcGGCGGcggcGGCGGUAauAGCGCcgUu -3' miRNA: 3'- -UGUa--UCGCCaa--CCGCCAU--UCGUGuaG- -5' |
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| 27505 | 3' | -51.6 | NC_005879.1 | + | 10885 | 0.66 | 0.76734 |
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Target: 5'- aGCAUaggcGGCGGcggcGGCGGUGGuGCAgCAUUg -3' miRNA: 3'- -UGUA----UCGCCaa--CCGCCAUU-CGU-GUAG- -5' |
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| 27505 | 3' | -51.6 | NC_005879.1 | + | 19173 | 0.66 | 0.766258 |
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Target: 5'- -aGUGGCaaaGUUGGCGGUacGAGCcauagcagauuccGCAUCu -3' miRNA: 3'- ugUAUCGc--CAACCGCCA--UUCG-------------UGUAG- -5' |
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| 27505 | 3' | -51.6 | NC_005879.1 | + | 3777 | 1.11 | 0.001017 |
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Target: 5'- aACAUAGCGGUUGGCGGUAAGCACAUCg -3' miRNA: 3'- -UGUAUCGCCAACCGCCAUUCGUGUAG- -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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