miRNA: 3'- cuggCCUGGaGUCCCUGGAG-CaCCUC- -5'
miRNA: 3'- -CUGGCCugGAGUCCCuGG-------------AGCACCuC- -5'
miRNA: 3'- cUGGCCUGGaGUCCCUGGagcaCCUC- -5'
miRNA: 3'- -CUGGCCUGGAGUCCCUGGa-----GCa----CCUC- -5'
miRNA: 3'- -CUGGCCUGGAGUCCCUGGAGCACCUC- -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 | |||||||
| 21937 | 5' | -59.7 | NC_004913.1 | + | 8671 | 0.68 | 0.407364 |
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Target: 5'- ---gGGGCCcCGGGGGCCUCaG-GGAGa -3' miRNA: 3'- cuggCCUGGaGUCCCUGGAG-CaCCUC- -5' |
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| 21937 | 5' | -59.7 | NC_004913.1 | + | 30377 | 0.68 | 0.38031 |
|
Target: 5'- aGGCCGGugUUCAGGG-CUguaucgaucguuaUCGUGGuGu -3' miRNA: 3'- -CUGGCCugGAGUCCCuGG-------------AGCACCuC- -5' |
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| 21937 | 5' | -59.7 | NC_004913.1 | + | 8994 | 0.76 | 0.126575 |
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Target: 5'- aGCCGGACCaCAGGGACCgaugGGAGc -3' miRNA: 3'- cUGGCCUGGaGUCCCUGGagcaCCUC- -5' |
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| 21937 | 5' | -59.7 | NC_004913.1 | + | 9608 | 0.85 | 0.025914 |
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Target: 5'- cGACCGGACCUCAGGGGCCgaagggCGacccgGGGGa -3' miRNA: 3'- -CUGGCCUGGAGUCCCUGGa-----GCa----CCUC- -5' |
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| 21937 | 5' | -59.7 | NC_004913.1 | + | 9092 | 1.08 | 0.000495 |
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Target: 5'- aGACCGGACCUCAGGGACCUCGUGGAGa -3' miRNA: 3'- -CUGGCCUGGAGUCCCUGGAGCACCUC- -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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