miRNA: 3'- ugCGUGC-GGaGUAGu-AUGAUCUAUGU- -5'
miRNA: 3'- -UGCGUGCGGa--GUAGuauga--UCUAUGU- -5'
miRNA: 3'- -UGCGUGCGGAGUaGUaUGaUCU---AUGu -5'
miRNA: 3'- -UGCGUGCGGAGUAGUAUGAUCUAUGU- -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 | |||||||
| 11860 | 5' | -49 | NC_003266.2 | + | 11928 | 0.66 | 0.880457 |
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Target: 5'- -gGCGCGaCCgUAUUuuUGCUAGAUGCAg -3' miRNA: 3'- ugCGUGC-GGaGUAGu-AUGAUCUAUGU- -5' |
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| 11860 | 5' | -49 | NC_003266.2 | + | 24179 | 0.67 | 0.854343 |
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Target: 5'- aGCGCGCGUCgccCAUCuccaaggAGAUGCAa -3' miRNA: 3'- -UGCGUGCGGa--GUAGuauga--UCUAUGU- -5' |
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| 11860 | 5' | -49 | NC_003266.2 | + | 10336 | 0.67 | 0.845074 |
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Target: 5'- uGCGCGCGCCUCA-CGgGCcAGAccgUGCc -3' miRNA: 3'- -UGCGUGCGGAGUaGUaUGaUCU---AUGu -5' |
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| 11860 | 5' | -49 | NC_003266.2 | + | 13853 | 1.09 | 0.002283 |
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Target: 5'- uACGCACGCCUCAUCAUACUAGAUACAa -3' miRNA: 3'- -UGCGUGCGGAGUAGUAUGAUCUAUGU- -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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