miRNA: 3'- -CAGAAGGaggaACCUGCCGg---UCGGUa -5'
miRNA: 3'- caGAAGGAGGaa--CC---UGCCGGUCGGua -5'
miRNA: 3'- cAGa---AGGAGGAACCUG--------C-CGgUCGGUA- -5'
miRNA: 3'- cAGAAGG--AGGAa-CCUgCCGg----UCGGUa -5'
miRNA: 3'- -CAGAAGGAGGAACCUGCCGGUCGGUA- -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 | |||||||
| 12684 | 5' | -57.8 | NC_003345.1 | + | 17850 | 0.66 | 0.605689 |
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Target: 5'- gGUCUUCCg---UGGACGGCauuaGGUCGg -3' miRNA: 3'- -CAGAAGGaggaACCUGCCGg---UCGGUa -5' |
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| 12684 | 5' | -57.8 | NC_003345.1 | + | 33178 | 0.67 | 0.573612 |
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Target: 5'- -gUUUCCUCCggcgGGuugGCGGUCGGCCc- -3' miRNA: 3'- caGAAGGAGGaa--CC---UGCCGGUCGGua -5' |
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| 12684 | 5' | -57.8 | NC_003345.1 | + | 52721 | 0.67 | 0.541947 |
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Target: 5'- cUCguagUCCUCCUUGGACuuguaccgGaGCgAGCCGUu -3' miRNA: 3'- cAGa---AGGAGGAACCUG--------C-CGgUCGGUA- -5' |
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| 12684 | 5' | -57.8 | NC_003345.1 | + | 44034 | 0.67 | 0.541947 |
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Target: 5'- aUCUUCCgcUCCUcgGGAgGGCagagaGGCCAg -3' miRNA: 3'- cAGAAGG--AGGAa-CCUgCCGg----UCGGUa -5' |
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| 12684 | 5' | -57.8 | NC_003345.1 | + | 75913 | 1.06 | 0.001213 |
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Target: 5'- gGUCUUCCUCCUUGGACGGCCAGCCAUa -3' miRNA: 3'- -CAGAAGGAGGAACCUGCCGGUCGGUA- -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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