miRNA: 3'- agaaCAACUGCGCUaUGUCGcuuguu -5'
miRNA: 3'- -AGAACAACu---GCGcuAUGUCGCUUGUU- -5'
miRNA: 3'- agAACAACU------------GCGCUAUGUCGC-UUGUu -5'
miRNA: 3'- agaaCAACugCGCUa--UGUCGCUUGUU- -5'
miRNA: 3'- -AGAACAACUGCGCUAUGUCGCUUGUU- -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 | |||||||
| 23526 | 5' | -48 | NC_005260.1 | + | 124869 | 0.66 | 0.999912 |
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Target: 5'- ---aGUUGACGCGAaACAGCu----- -3' miRNA: 3'- agaaCAACUGCGCUaUGUCGcuuguu -5' |
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| 23526 | 5' | -48 | NC_005260.1 | + | 56243 | 0.68 | 0.999082 |
|
Target: 5'- aUCUUGUUGccuuCGU--UGCAGUGGACAGc -3' miRNA: 3'- -AGAACAACu---GCGcuAUGUCGCUUGUU- -5' |
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| 23526 | 5' | -48 | NC_005260.1 | + | 201331 | 0.69 | 0.997644 |
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Target: 5'- -gUUGUUGAuacugucuuuggUGUGAUGCAGCGcAACAu -3' miRNA: 3'- agAACAACU------------GCGCUAUGUCGC-UUGUu -5' |
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| 23526 | 5' | -48 | NC_005260.1 | + | 205854 | 0.76 | 0.895733 |
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Target: 5'- ---cGUUGugGCGAagaACGGCGAGCGAc -3' miRNA: 3'- agaaCAACugCGCUa--UGUCGCUUGUU- -5' |
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| 23526 | 5' | -48 | NC_005260.1 | + | 182755 | 1.07 | 0.028951 |
|
Target: 5'- aUCUUGUUGACGCGAUACAGCGAACAAc -3' miRNA: 3'- -AGAACAACUGCGCUAUGUCGCUUGUU- -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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