miRNA: 3'- -GACCGa----UGG---UUGGUU-------------CGGUUCGUUGa -5'
miRNA: 3'- gaCCGAUGGU------UGGU---UCGGU------------UCGUUGa -5'
miRNA: 3'- -GACCGAUGGUUGGUUCGGUUCGUUGA- -5'
Results 1 - 3 of 3 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 | |||||||
| 21838 | 5' | -52 | NC_004831.2 | + | 10505 | 0.66 | 0.755496 |
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Target: 5'- aCUGGCguuacACUuggAGCCGAugcuuucauucauGCCGAGCGGCg -3' miRNA: 3'- -GACCGa----UGG---UUGGUU-------------CGGUUCGUUGa -5' |
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| 21838 | 5' | -52 | NC_004831.2 | + | 38164 | 0.73 | 0.391205 |
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Target: 5'- -cGGCUGCCAgaugcaACCAcaaGGCCAugcuugucugucAGCAGCa -3' miRNA: 3'- gaCCGAUGGU------UGGU---UCGGU------------UCGUUGa -5' |
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| 21838 | 5' | -52 | NC_004831.2 | + | 22805 | 1.09 | 0.001319 |
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Target: 5'- gCUGGCUACCAACCAAGCCAAGCAACUg -3' miRNA: 3'- -GACCGAUGGUUGGUUCGGUUCGUUGA- -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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