miRNA: 3'- uagGUAgCGGUUCGaaGAG----AGGUUGc -5'
miRNA: 3'- -UAGGuAGCGGUUCGa--AG-AGaGGUUGc -5'
miRNA: 3'- -UAGGUAGCGGUUCGAaga---GAGGuUGC- -5'
miRNA: 3'- uaGGUAGCGGUUCGA--AGa--GAGG-----UUGC- -5'
miRNA: 3'- -UAGGUAGCGGUUCGAAGAGAGGUUGC- -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 | |||||||
| 8326 | 3' | -52.4 | NC_002067.1 | + | 25489 | 0.66 | 0.681989 |
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Target: 5'- --gCAUgGCCGAGCggCUCcgcaUCCAGCa -3' miRNA: 3'- uagGUAgCGGUUCGaaGAG----AGGUUGc -5' |
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| 8326 | 3' | -52.4 | NC_002067.1 | + | 25328 | 0.69 | 0.542043 |
|
Target: 5'- cAUCC-UCGCCGAGCgcgUCgUCgCCGACc -3' miRNA: 3'- -UAGGuAGCGGUUCGa--AG-AGaGGUUGc -5' |
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| 8326 | 3' | -52.4 | NC_002067.1 | + | 28254 | 0.72 | 0.346712 |
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Target: 5'- aGUUCGUCGCCAAGCUgcaagaCUCCuACGc -3' miRNA: 3'- -UAGGUAGCGGUUCGAaga---GAGGuUGC- -5' |
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| 8326 | 3' | -52.4 | NC_002067.1 | + | 26027 | 0.74 | 0.273411 |
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Target: 5'- -aCCAUCGCCGAGCUcaUCaggCUCCuggaaGACGa -3' miRNA: 3'- uaGGUAGCGGUUCGA--AGa--GAGG-----UUGC- -5' |
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| 8326 | 3' | -52.4 | NC_002067.1 | + | 28982 | 1.07 | 0.001401 |
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Target: 5'- gAUCCAUCGCCAAGCUUCUCUCCAACGc -3' miRNA: 3'- -UAGGUAGCGGUUCGAAGAGAGGUUGC- -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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