miRNA: 3'- -UGCUcGUc-CGGCGCGCcCGCAAGCUG- -5'
miRNA: 3'- uGC-UCGUCCGGC----GCG--CCCGCA-----------AGCUG- -5'
miRNA: 3'- -UGCUCGUc--CGGC-GCGCCCGCa---AGCUg -5'
miRNA: 3'- -UGCU-CGUcCGGCGCGCCCG-----CAAGcug -5'
miRNA: 3'- -UGCUCGUcCGGCGCGCCcgCa-AGCUG- -5'
Results 1 - 5 of 5 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 | |||||||
| 12231 | 5' | -61.9 | NC_003309.1 | + | 17810 | 0.66 | 0.389758 |
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Target: 5'- gGCGAuCGucGCCGUGUGcGCGUUCGGCg -3' miRNA: 3'- -UGCUcGUc-CGGCGCGCcCGCAAGCUG- -5' |
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| 12231 | 5' | -61.9 | NC_003309.1 | + | 25549 | 0.67 | 0.324546 |
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Target: 5'- gUGuAGCGGGCCGaagaCGCacGGGCGUcguuucgccuuUCGGCg -3' miRNA: 3'- uGC-UCGUCCGGC----GCG--CCCGCA-----------AGCUG- -5' |
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| 12231 | 5' | -61.9 | NC_003309.1 | + | 34533 | 0.67 | 0.302275 |
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Target: 5'- aGCGAGCAcccGUCGaUGUGGGCGgccgUCGAa -3' miRNA: 3'- -UGCUCGUc--CGGC-GCGCCCGCa---AGCUg -5' |
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| 12231 | 5' | -61.9 | NC_003309.1 | + | 47340 | 0.68 | 0.288093 |
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Target: 5'- cGCGGcGCAcGCCGCGCGGGUugaugGUUCu-- -3' miRNA: 3'- -UGCU-CGUcCGGCGCGCCCG-----CAAGcug -5' |
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| 12231 | 5' | -61.9 | NC_003309.1 | + | 41373 | 0.72 | 0.140889 |
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Target: 5'- gGCGGGCAaGCCGCGUGGuuGgcUCGACa -3' miRNA: 3'- -UGCUCGUcCGGCGCGCCcgCa-AGCUG- -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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