miRNA: 3'- gUCGGA--AGCGU--------GCGCCUCCGCCGcGU- -5'
miRNA: 3'- guCGGa-AGCGugCGCcUCCGC-----------CGCGU- -5'
miRNA: 3'- -GUCGGaag--CGUGCgCCUCCGCCgCGU- -5'
miRNA: 3'- -GUCGGAa-----------GCGuGcGCCUCCGCCGCGU- -5'
Results 21 - 24 of 24 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand |
Start Position
|
R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 13438 | 3' | -62.2 | NC_003409.1 | + | 111840 | 0.66 | 0.595082 |
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Target: 5'- gGGUUUccUCGCGucggccacCGCGGGGGCGGC-CGu -3' miRNA: 3'- gUCGGA--AGCGU--------GCGCCUCCGCCGcGU- -5' |
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| 13438 | 3' | -62.2 | NC_003409.1 | + | 113593 | 0.66 | 0.575335 |
|
Target: 5'- -cGCCcgUCGCugGCGcAGGCGaucgccguguuGCGCGu -3' miRNA: 3'- guCGGa-AGCGugCGCcUCCGC-----------CGCGU- -5' |
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| 13438 | 3' | -62.2 | NC_003409.1 | + | 131249 | 0.73 | 0.24038 |
|
Target: 5'- gCGGCCacacgGCGCGgGGAGGUGGgGCAc -3' miRNA: 3'- -GUCGGaag--CGUGCgCCUCCGCCgCGU- -5' |
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| 13438 | 3' | -62.2 | NC_003409.1 | + | 134492 | 0.66 | 0.573367 |
|
Target: 5'- gCAGCCUgacuacagagggUGUcCcCGGGGGCGGUGCGc -3' miRNA: 3'- -GUCGGAa-----------GCGuGcGCCUCCGCCGCGU- -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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