miRNA: 3'- -GGUUGAUAGGGAUGGGAGAAUAUCCG- -5'
miRNA: 3'- gGUUGAUAGGGa----------UGGGAGa--A-------------UAUCCG- -5'
miRNA: 3'- -GGUUGAua-GGGAuGGGAGAAuauCCG- -5'
miRNA: 3'- -GGUUGauaGGG-------AUGGGAGaau----AUCCG- -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 | |||||||
| 2540 | 5' | -48 | NC_001460.1 | + | 20150 | 1.15 | 0.001468 |
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Target: 5'- gCCAACUAUCCCUACCCUCUUAUAGGCc -3' miRNA: 3'- -GGUUGAUAGGGAUGGGAGAAUAUCCG- -5' |
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| 2540 | 5' | -48 | NC_001460.1 | + | 10648 | 0.68 | 0.861997 |
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Target: 5'- gCGACUGUCCCgggcgagcugcACCCUUgggUgacgcucaggagaGUGGGCg -3' miRNA: 3'- gGUUGAUAGGGa----------UGGGAGa--A-------------UAUCCG- -5' |
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| 2540 | 5' | -48 | NC_001460.1 | + | 25786 | 0.68 | 0.888112 |
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Target: 5'- aUCAACUuaaCCCU-CCCUCUU---GGCc -3' miRNA: 3'- -GGUUGAua-GGGAuGGGAGAAuauCCG- -5' |
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| 2540 | 5' | -48 | NC_001460.1 | + | 19602 | 0.66 | 0.935456 |
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Target: 5'- aCCAGCgugCCCauuucaaUACCUUCgcgaaauUGGGCg -3' miRNA: 3'- -GGUUGauaGGG-------AUGGGAGaau----AUCCG- -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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