miRNA: 3'- -CGC-GACuuUCuACGACCGgaaUUGCa -5'
miRNA: 3'- -CGCGACUuuCUACGAC--------CGGAA------UUGCa -5'
miRNA: 3'- -CGCGACUUUCuaCGACCGgaaUUGca -5'
miRNA: 3'- -CGCGACUUUCUACGACCGGAAUUGCA- -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 | |||||||
| 21149 | 5' | -50 | NC_004775.1 | + | 14318 | 0.66 | 0.876766 |
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Target: 5'- cGCGcCUGggGGuUGUUGGCg--AACGa -3' miRNA: 3'- -CGC-GACuuUCuACGACCGgaaUUGCa -5' |
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| 21149 | 5' | -50 | NC_004775.1 | + | 38541 | 0.72 | 0.573309 |
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Target: 5'- gGCGCUGAuuGAUGCUGgauucagaGCCUUcccgccAGCGc -3' miRNA: 3'- -CGCGACUuuCUACGAC--------CGGAA------UUGCa -5' |
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| 21149 | 5' | -50 | NC_004775.1 | + | 34284 | 0.72 | 0.573309 |
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Target: 5'- cGCGCUGAAAG--GCUGGCacgGGCa- -3' miRNA: 3'- -CGCGACUUUCuaCGACCGgaaUUGca -5' |
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| 21149 | 5' | -50 | NC_004775.1 | + | 14505 | 1.1 | 0.001902 |
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Target: 5'- gGCGCUGAAAGAUGCUGGCCUUAACGUc -3' miRNA: 3'- -CGCGACUUUCUACGACCGGAAUUGCA- -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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