miRNA: 3'- -GUUGCGGUAGC-Guc-----AGGUuGGGUAGc -5'
miRNA: 3'- gUUGCGGUAG-CGUCAGgUUGGG--UAGc -5'
miRNA: 3'- gUUGCGGUAGCGUCagguUGGGUa--Gc -5'
miRNA: 3'- -GUUGCGgUAGCGUc--AGGUU-GGGUAGC- -5'
miRNA: 3'- -GUUGCGGUAGCGUCAGGUUGGGUAGC- -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 | |||||||
| 31555 | 3' | -53.7 | NC_006820.1 | + | 135447 | 0.66 | 0.98089 |
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Target: 5'- gCAACGCCAUCGgCcuucacuUCUAuCCCAUCu -3' miRNA: 3'- -GUUGCGGUAGC-Guc-----AGGUuGGGUAGc -5' |
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| 31555 | 3' | -53.7 | NC_006820.1 | + | 40594 | 0.66 | 0.973782 |
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Target: 5'- aGACGCCAUUaGUAGUUgAACCUguAUCu -3' miRNA: 3'- gUUGCGGUAG-CGUCAGgUUGGG--UAGc -5' |
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| 31555 | 3' | -53.7 | NC_006820.1 | + | 136270 | 0.67 | 0.961558 |
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Target: 5'- gAACGCCAUCGUAGauacGCCCAgggCa -3' miRNA: 3'- gUUGCGGUAGCGUCagguUGGGUa--Gc -5' |
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| 31555 | 3' | -53.7 | NC_006820.1 | + | 138106 | 0.67 | 0.95416 |
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Target: 5'- aCAACGCaAUCGCAuucUCUGGuCCCAUCGc -3' miRNA: 3'- -GUUGCGgUAGCGUc--AGGUU-GGGUAGC- -5' |
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| 31555 | 3' | -53.7 | NC_006820.1 | + | 23484 | 1.08 | 0.007228 |
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Target: 5'- cCAACGCCAUCGCAGUCCAACCCAUCGc -3' miRNA: 3'- -GUUGCGGUAGCGUCAGGUUGGGUAGC- -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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