miRNA: 3'- -UGGcUCGAAGCGUCUUaCGAU-GUGGU- -5'
miRNA: 3'- -UGGCuCGaa-GCGUCUUaCGAUG---UGGU- -5'
miRNA: 3'- -UGGCUCGaa-GCGUCUUa---CGa-UGUGGU- -5'
miRNA: 3'- -UGGCUCGAAGCGUCUUACGAUGUGGU- -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 | |||||||
| 2640 | 3' | -52.6 | NC_001491.2 | + | 66773 | 0.66 | 0.962632 |
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Target: 5'- uGCU-AGCUUCGCAGGA-GCUAgUAUCAa -3' miRNA: 3'- -UGGcUCGAAGCGUCUUaCGAU-GUGGU- -5' |
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| 2640 | 3' | -52.6 | NC_001491.2 | + | 10437 | 0.68 | 0.937012 |
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Target: 5'- cGCCG-GCggaCGCAGAGcGCUACuggGCCGc -3' miRNA: 3'- -UGGCuCGaa-GCGUCUUaCGAUG---UGGU- -5' |
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| 2640 | 3' | -52.6 | NC_001491.2 | + | 12543 | 0.73 | 0.698277 |
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Target: 5'- gACCGAGCgggCGCGGGAgcgcGCgaGCGCCGc -3' miRNA: 3'- -UGGCUCGaa-GCGUCUUa---CGa-UGUGGU- -5' |
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| 2640 | 3' | -52.6 | NC_001491.2 | + | 129473 | 1.09 | 0.005443 |
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Target: 5'- uACCGAGCUUCGCAGAAUGCUACACCAa -3' miRNA: 3'- -UGGCUCGAAGCGUCUUACGAUGUGGU- -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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