miRNA: 3'- caUAGAG---GCUCAGcCUCA---UGGCCGUu -5'
miRNA: 3'- caUAGa----GGCUCAGCC----UCA---UGGCCGUU- -5'
miRNA: 3'- caUAGAGGC---UCAGCCUCa--UGgCCGUu -5'
miRNA: 3'- -CAUAGAGGCUCAGCc---UCAUGGCCGUU- -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 | |||||||
| 22141 | 5' | -54.9 | NC_004927.1 | + | 36414 | 0.66 | 0.812675 |
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Target: 5'- -cGUCUCuauCGGGUCaGAGUguuGCCGGUAc -3' miRNA: 3'- caUAGAG---GCUCAGcCUCA---UGGCCGUu -5' |
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| 22141 | 5' | -54.9 | NC_004927.1 | + | 21747 | 0.66 | 0.774148 |
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Target: 5'- -cGUCgccgcCCGAGUUGGcgauAGUgauACCGGCGAa -3' miRNA: 3'- caUAGa----GGCUCAGCC----UCA---UGGCCGUU- -5' |
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| 22141 | 5' | -54.9 | NC_004927.1 | + | 23236 | 0.69 | 0.64761 |
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Target: 5'- -cGUCUCCGcucGGUCGGGGagaGCgGGCGu -3' miRNA: 3'- caUAGAGGC---UCAGCCUCa--UGgCCGUu -5' |
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| 22141 | 5' | -54.9 | NC_004927.1 | + | 42618 | 0.8 | 0.149188 |
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Target: 5'- cGUGUCUCCGGGUCGaaguAGUGCUGGUAGa -3' miRNA: 3'- -CAUAGAGGCUCAGCc---UCAUGGCCGUU- -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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