miRNA: 3'- cgCGGGUCGggCCCCgAGuAGGGAag -5'
miRNA: 3'- -CGCGGG--UCGG-GC-CCCGAGuaGGGAAG- -5'
miRNA: 3'- -CGCGGGuCGG---GCCCCGa---GUA-GGGaag -5'
miRNA: 3'- -CGCGGGu--------CGGGCCCCGAGU--AGGGaag -5'
miRNA: 3'- -CGCGGGUCGGGCCCCGAGUAGGGAAG- -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 | |||||||
| 31611 | 5' | -62.6 | NC_006879.1 | + | 19540 | 0.66 | 0.254802 |
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Target: 5'- -aGCCCAGCgaGGGGgUC-UCCUUg- -3' miRNA: 3'- cgCGGGUCGggCCCCgAGuAGGGAag -5' |
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| 31611 | 5' | -62.6 | NC_006879.1 | + | 4773 | 0.66 | 0.24207 |
|
Target: 5'- gGCGUCCagGGCCgCGaGGGUUCugUCCUUCc -3' miRNA: 3'- -CGCGGG--UCGG-GC-CCCGAGuaGGGAAG- -5' |
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| 31611 | 5' | -62.6 | NC_006879.1 | + | 9989 | 0.66 | 0.22397 |
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Target: 5'- uGCGCCC-GCCucaCGGGGCagagCGUgCCCa-- -3' miRNA: 3'- -CGCGGGuCGG---GCCCCGa---GUA-GGGaag -5' |
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| 31611 | 5' | -62.6 | NC_006879.1 | + | 22268 | 0.74 | 0.064556 |
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Target: 5'- gGCGCCUccugcucgcGCUCGGGGCUCAucUCCCg-- -3' miRNA: 3'- -CGCGGGu--------CGGGCCCCGAGU--AGGGaag -5' |
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| 31611 | 5' | -62.6 | NC_006879.1 | + | 4904 | 1.11 | 0.000066 |
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Target: 5'- aGCGCCCAGCCCGGGGCUCAUCCCUUCa -3' miRNA: 3'- -CGCGGGUCGGGCCCCGAGUAGGGAAG- -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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