miRNA: 3'- -UAUCu-UCCaaCGGUG-------------UCCGGGggCCU- -5'
miRNA: 3'- uaUCUUCCa--ACG-GUG-UCCGGGGGccu -5'
miRNA: 3'- -UAUCUUCCa---------ACGgug-------UCCGGGGGCCU- -5'
miRNA: 3'- -UAUCUUCCAACGGUGUCCGGGGGCCU- -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 | |||||||
| 22451 | 3' | -58.5 | NC_005062.1 | + | 9089 | 0.67 | 0.124664 |
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Target: 5'- uGUGGcuGGGgaGCCGCuuucuggaguuugAGGCCCuuGGAu -3' miRNA: 3'- -UAUCu-UCCaaCGGUG-------------UCCGGGggCCU- -5' |
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| 22451 | 3' | -58.5 | NC_005062.1 | + | 8305 | 0.67 | 0.110231 |
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Target: 5'- -gAGAAGGgagUGCgCACuAGGCCUCCa-- -3' miRNA: 3'- uaUCUUCCa--ACG-GUG-UCCGGGGGccu -5' |
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| 22451 | 3' | -58.5 | NC_005062.1 | + | 10556 | 0.7 | 0.06552 |
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Target: 5'- cAUGGAAGGccaaacauggUGCaugaagggaaAGGCCCCCGGAa -3' miRNA: 3'- -UAUCUUCCa---------ACGgug-------UCCGGGGGCCU- -5' |
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| 22451 | 3' | -58.5 | NC_005062.1 | + | 6137 | 1.07 | 5.1e-05 |
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Target: 5'- cAUAGAAGGUUGCCACAGGCCCCCGGAg -3' miRNA: 3'- -UAUCUUCCAACGGUGUCCGGGGGCCU- -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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