miRNA: 3'- -UAGUGGUCAUGGGGCAUGUCGUUUUC- -5'
miRNA: 3'- uaGUGG----UCAUGGGG---CAUGUCGUUUUC- -5'
miRNA: 3'- -UAGUGGUCAUGGGGCAuguCGuUUUC- -5'
miRNA: 3'- uagUGGUCA---UGGGGCaUGUCGU-UUUC- -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 | |||||||
| 16543 | 5' | -50.7 | NC_004104.1 | + | 5029 | 1.07 | 0.000242 |
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Target: 5'- cAUCACCAGUACCCCGUACAGCAAAAGu -3' miRNA: 3'- -UAGUGGUCAUGGGGCAUGUCGUUUUC- -5' |
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| 16543 | 5' | -50.7 | NC_004104.1 | + | 5297 | 0.71 | 0.157524 |
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Target: 5'- -gUACCggacGGUACCCCugcGUGCAGUAAGGGc -3' miRNA: 3'- uaGUGG----UCAUGGGG---CAUGUCGUUUUC- -5' |
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| 16543 | 5' | -50.7 | NC_004104.1 | + | 5026 | 0.67 | 0.326079 |
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Target: 5'- uAUUAUUAGUACCCCGUu--GCcAGGGg -3' miRNA: 3'- -UAGUGGUCAUGGGGCAuguCGuUUUC- -5' |
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| 16543 | 5' | -50.7 | NC_004104.1 | + | 3432 | 0.66 | 0.355957 |
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Target: 5'- --gACCAGUguaACCCUG-ACAGCGcAAAGc -3' miRNA: 3'- uagUGGUCA---UGGGGCaUGUCGU-UUUC- -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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