miRNA: 3'- aAGAGAGU-----CCGGA-------------GGUGUCCgGCGGG- -5'
miRNA: 3'- aAGAGAGU-----CCGGA-------------GGUGUCCgGCGGG- -5'
miRNA: 3'- -AAGAGAGUCCGGAGGUGUCCGGCGGG- -5'
miRNA: 3'- -AAGAGAGUCCGGAGGUGUCCGGCGGG- -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 | |||||||
| 21818 | 3' | -61.2 | NC_004831.2 | + | 1 | 0.67 | 0.255484 |
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Target: 5'- -UCUCUCGgccucGGCCUcgccgggauguccCCAUAGGgUGCCUg -3' miRNA: 3'- aAGAGAGU-----CCGGA-------------GGUGUCCgGCGGG- -5' |
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| 21818 | 3' | -61.2 | NC_004831.2 | + | 43552 | 0.68 | 0.249036 |
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Target: 5'- cUCUCUCGgccucGGCCUcgccgggauguccCCAUAGGgUGCCUg -3' miRNA: 3'- aAGAGAGU-----CCGGA-------------GGUGUCCgGCGGG- -5' |
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| 21818 | 3' | -61.2 | NC_004831.2 | + | 43675 | 1.08 | 0.000183 |
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Target: 5'- cUUCUCUCAGGCCUCCACAGGCCGCCCu -3' miRNA: 3'- -AAGAGAGUCCGGAGGUGUCCGGCGGG- -5' |
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| 21818 | 3' | -61.2 | NC_004831.2 | + | 123 | 1.08 | 0.000183 |
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Target: 5'- cUUCUCUCAGGCCUCCACAGGCCGCCCu -3' miRNA: 3'- -AAGAGAGUCCGGAGGUGUCCGGCGGG- -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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