miRNA: 3'- uAGUGGCA----AGUccUUUCGGCGGCAca -5'
miRNA: 3'- -UAGUgGCa------AGUCCUUUCGGCGGCAca -5'
miRNA: 3'- -UAgUGGCaaGUCCUUUCG-GCGGcaca -5'
miRNA: 3'- -UAGUGGCAAGUCCUUUCGGCGGCACA- -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 | |||||||
| 22057 | 3' | -55 | NC_004927.1 | + | 2092 | 0.66 | 0.80011 |
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Target: 5'- uUCACCGUauucUCAacGAAGUCGCCGUc- -3' miRNA: 3'- uAGUGGCA----AGUccUUUCGGCGGCAca -5' |
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| 22057 | 3' | -55 | NC_004927.1 | + | 23264 | 0.68 | 0.697884 |
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Target: 5'- cGUCGgCGggagugaUUAGGAGAGUCGCCGUc- -3' miRNA: 3'- -UAGUgGCa------AGUCCUUUCGGCGGCAca -5' |
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| 22057 | 3' | -55 | NC_004927.1 | + | 24319 | 0.68 | 0.654617 |
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Target: 5'- uGUgGCCGgaCAGGGAAGCuCGCCa--- -3' miRNA: 3'- -UAgUGGCaaGUCCUUUCG-GCGGcaca -5' |
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| 22057 | 3' | -55 | NC_004927.1 | + | 31686 | 1.05 | 0.002825 |
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Target: 5'- uAUCACCGUUCAGGAAAGCCGCCGUGUc -3' miRNA: 3'- -UAGUGGCAAGUCCUUUCGGCGGCACA- -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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