miRNA: 3'- aaGUAauUGUGCUUCGUC-ACGCUGaa -5'
miRNA: 3'- aaGUA-AUUGugCUUCGUC---------------ACGCUGAa -5'
miRNA: 3'- aaGUAAUUGugCuuCGUCa--------------CGCUGaa -5'
miRNA: 3'- -AAGUAAUUGUGCUUCGUCACGCUGAA- -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 | |||||||
| 13392 | 5' | -47.9 | NC_003409.1 | + | 117141 | 0.67 | 0.995723 |
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Target: 5'- -cCAU--AUGCGAAGCGGuUGCGGCg- -3' miRNA: 3'- aaGUAauUGUGCUUCGUC-ACGCUGaa -5' |
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| 13392 | 5' | -47.9 | NC_003409.1 | + | 73040 | 0.68 | 0.992462 |
|
Target: 5'- -aCAUaUGGCugGAGGCAGgcucaccccgcugcaUGCGGCUg -3' miRNA: 3'- aaGUA-AUUGugCUUCGUC---------------ACGCUGAa -5' |
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| 13392 | 5' | -47.9 | NC_003409.1 | + | 129150 | 0.69 | 0.984372 |
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Target: 5'- -aCGUUGGCugGggGCAGggcaaaacccaaaacGCGACa- -3' miRNA: 3'- aaGUAAUUGugCuuCGUCa--------------CGCUGaa -5' |
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| 13392 | 5' | -47.9 | NC_003409.1 | + | 52215 | 1.03 | 0.028437 |
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Target: 5'- gUUCAUUAACACGAAGCAGUGCGACUUu -3' miRNA: 3'- -AAGUAAUUGUGCUUCGUCACGCUGAA- -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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