miRNA: 3'- uCCaCCUGACCCa-GAGGUCCGa---GAac -5'
miRNA: 3'- -UCCaCCUGa-CCCAGAGGuCCGaGAac -5'
miRNA: 3'- -UCCaCCuGACCCA---GAgGUCCGAGaAC- -5'
miRNA: 3'- -UCCaCCUGACCC---AGAGGu----CCGAGaac -5'
miRNA: 3'- -UCCACCUGACCCAGAGGUCCGAGAAC- -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 | |||||||
| 19845 | 5' | -57.6 | NC_004687.1 | + | 106939 | 0.66 | 0.833344 |
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Target: 5'- cGG-GGACUGGGagUUCCAGGUccggCUg- -3' miRNA: 3'- uCCaCCUGACCCa-GAGGUCCGa---GAac -5' |
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| 19845 | 5' | -57.6 | NC_004687.1 | + | 130970 | 0.66 | 0.816447 |
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Target: 5'- uGGGaGGACcgGGGUCUCC-GGCcCUc- -3' miRNA: 3'- -UCCaCCUGa-CCCAGAGGuCCGaGAac -5' |
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| 19845 | 5' | -57.6 | NC_004687.1 | + | 81860 | 0.67 | 0.789878 |
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Target: 5'- cGGGcGGuCUGGGUgccCUgCGGGCUCaUGg -3' miRNA: 3'- -UCCaCCuGACCCA---GAgGUCCGAGaAC- -5' |
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| 19845 | 5' | -57.6 | NC_004687.1 | + | 96442 | 0.67 | 0.771447 |
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Target: 5'- cGGGaGGGCUGGGaggUCUCCccugcGGCUCc-- -3' miRNA: 3'- -UCCaCCUGACCC---AGAGGu----CCGAGaac -5' |
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| 19845 | 5' | -57.6 | NC_004687.1 | + | 66111 | 1.08 | 0.002077 |
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Target: 5'- aAGGUGGACUGGGUCUCCAGGCUCUUGa -3' miRNA: 3'- -UCCACCUGACCCAGAGGUCCGAGAAC- -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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