miRNA: 3'- -CUGAGUCGUC---AGUCUCUGU-----------UAGUGaa -5'
miRNA: 3'- -CUGAGUCGUCagu---CUCUGUUAGuGAa -5'
miRNA: 3'- cUGAGUCGUCAGUcUCUGUUaGUGAA- -5'
miRNA: 3'- -CUGAGUCGUCAGUCUCUGUUAGUGAA- -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 | |||||||
| 3993 | 5' | -50 | NC_001650.1 | + | 28242 | 0.66 | 0.995884 |
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Target: 5'- gGGCUCGGUGGuguUCAGGGACAgccuggccaacGUCAUg- -3' miRNA: 3'- -CUGAGUCGUC---AGUCUCUGU-----------UAGUGaa -5' |
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| 3993 | 5' | -50 | NC_001650.1 | + | 99649 | 0.72 | 0.917188 |
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Target: 5'- aGGCUCAGCAGguugacGAGACAGUCcCUc -3' miRNA: 3'- -CUGAGUCGUCagu---CUCUGUUAGuGAa -5' |
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| 3993 | 5' | -50 | NC_001650.1 | + | 57534 | 0.76 | 0.71923 |
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Target: 5'- aACUCGGCAGUCAuGGGCAGcCACUUu -3' miRNA: 3'- cUGAGUCGUCAGUcUCUGUUaGUGAA- -5' |
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| 3993 | 5' | -50 | NC_001650.1 | + | 126718 | 1.06 | 0.017003 |
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Target: 5'- cGACUCAGCAGUCAGAGACAAUCACUUu -3' miRNA: 3'- -CUGAGUCGUCAGUCUCUGUUAGUGAA- -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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