miRNA: 3'- -CGCCGgCUCGGCcAGUcaacGGGCUC- -5'
miRNA: 3'- -CGC-CGGcuCGGCCa--------GUC---AACGGGCUC- -5'
miRNA: 3'- -CGccGGCUCGGCCAGUCa-------------ACGGGCUC- -5'
miRNA: 3'- -CGCCGGCUCGGCCAGUCAACGGGCUC- -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 |
| Predicted miRNA align pattern | |||||||
| 12187 | 3' | -60.8 | NC_003309.1 | + | 19444 | 0.67 | 0.37105 |
|
Target: 5'- cGCGGCgGAGCCG-UCA----CCCGGGa -3' miRNA: 3'- -CGCCGgCUCGGCcAGUcaacGGGCUC- -5' |
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| 12187 | 3' | -60.8 | NC_003309.1 | + | 28483 | 0.66 | 0.432898 |
|
Target: 5'- cGCGcGCCacGCCGGcccguauagCGGcgaUUGCCCGAGg -3' miRNA: 3'- -CGC-CGGcuCGGCCa--------GUC---AACGGGCUC- -5' |
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| 12187 | 3' | -60.8 | NC_003309.1 | + | 35827 | 0.67 | 0.357784 |
|
Target: 5'- cGCauUCGAGCUGGUCGGcgcaaucgacuuacUGCCCGAGu -3' miRNA: 3'- -CGccGGCUCGGCCAGUCa-------------ACGGGCUC- -5' |
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| 12187 | 3' | -60.8 | NC_003309.1 | + | 49940 | 1.09 | 0.000319 |
|
Target: 5'- gGCGGCCGAGCCGGUCAGUUGCCCGAGc -3' miRNA: 3'- -CGCCGGCUCGGCCAGUCAACGGGCUC- -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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