miRNA: 3'- -CGA-UUUCA--AAGCAAaa--GGUU-GUCUGC- -5'
miRNA: 3'- cgAUUUCAaaGCAA--AAGGUUGUCUGC- -5'
miRNA: 3'- -CGauUUCAaaGCAAAAG---------GUUGUCUGC- -5'
miRNA: 3'- cgaUUUCA-AAGCAAAAGGUUG--UCUGc -5'
miRNA: 3'- -CGAUUUCAAAGCAAAAGGUUGUCUGC- -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 | |||||||
| 3426 | 5' | -41.2 | NC_001598.1 | + | 8954 | 0.66 | 0.994466 |
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Target: 5'- uGCUcAAAGUuuUUCGUUaugaCCGGuCAGACGu -3' miRNA: 3'- -CGA-UUUCA--AAGCAAaa--GGUU-GUCUGC- -5' |
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| 3426 | 5' | -41.2 | NC_001598.1 | + | 6381 | 0.67 | 0.99055 |
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Target: 5'- -gUAGAGUa-CGUUugUUUCGACGGGCGg -3' miRNA: 3'- cgAUUUCAaaGCAA--AAGGUUGUCUGC- -5' |
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| 3426 | 5' | -41.2 | NC_001598.1 | + | 14186 | 0.69 | 0.961038 |
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Target: 5'- cGUguGAGUggCGUUUUCgcgcgcuaaCAGCAGACGa -3' miRNA: 3'- -CGauUUCAaaGCAAAAG---------GUUGUCUGC- -5' |
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| 3426 | 5' | -41.2 | NC_001598.1 | + | 636 | 0.75 | 0.743456 |
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Target: 5'- --gAAAGUaUUCGUUUUCCAACgaAGACu -3' miRNA: 3'- cgaUUUCA-AAGCAAAAGGUUG--UCUGc -5' |
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| 3426 | 5' | -41.2 | NC_001598.1 | + | 2202 | 1.16 | 0.003323 |
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Target: 5'- gGCUAAAGUUUCGUUUUCCAACAGACGg -3' miRNA: 3'- -CGAUUUCAAAGCAAAAGGUUGUCUGC- -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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