miRNA: 3'- aUCUCguCCAUCuGGG------CCUUGugGUa -5'
miRNA: 3'- -AUCUCGUCc--AUCUGgGCCU-----UGUGGUA- -5'
miRNA: 3'- aUCUCGU-CC------AUCUGGGCCUUGU--------GGUA- -5'
miRNA: 3'- -AUCUCGUCCAUCUGGGCCUUGUGGUA- -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 | |||||||
| 497 | 3' | -55.7 | AC_000013.1 | + | 33916 | 0.66 | 0.588827 |
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Target: 5'- aGGAGguGGUAG-CCCuuaccaGGGGCugCGg -3' miRNA: 3'- aUCUCguCCAUCuGGG------CCUUGugGUa -5' |
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| 497 | 3' | -55.7 | AC_000013.1 | + | 15190 | 0.67 | 0.522078 |
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Target: 5'- uUAGGGCGGacaUAGACgCGGAgggagACGCCGUg -3' miRNA: 3'- -AUCUCGUCc--AUCUGgGCCU-----UGUGGUA- -5' |
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| 497 | 3' | -55.7 | AC_000013.1 | + | 6631 | 0.73 | 0.240126 |
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Target: 5'- aAGAGCAcGGagacgcUAGACCCGGAGCAgaguuuauCCAUg -3' miRNA: 3'- aUCUCGU-CC------AUCUGGGCCUUGU--------GGUA- -5' |
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| 497 | 3' | -55.7 | AC_000013.1 | + | 37409 | 1.03 | 0.001348 |
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Target: 5'- gUAGAGCAGGUAGACCCGGAACACCAUu -3' miRNA: 3'- -AUCUCGUCCAUCUGGGCCUUGUGGUA- -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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