miRNA: 3'- uaAAGUCGUCGa-GGACG-----------UGGaGGCuC- -5'
miRNA: 3'- uaaaGUCGUCGAGg---ACGuGGAGGCUC- -5'
miRNA: 3'- uaaaGUCGUCG------------AGGaCGUGGAGGCUc -5'
miRNA: 3'- uaaaGUCGUCGAGGACGUGGAGGCUC- -5'
miRNA: 3'- -UAAAGUCGUCGAGGACGUGGAGGCUC- -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 | |||||||
| 2210 | 3' | -55.4 | NC_001403.1 | + | 3181 | 0.66 | 0.093737 |
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Target: 5'- -gUUCAGCGGCcgCCUGCgugcugacaacACCcCCGuGg -3' miRNA: 3'- uaAAGUCGUCGa-GGACG-----------UGGaGGCuC- -5' |
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| 2210 | 3' | -55.4 | NC_001403.1 | + | 1508 | 0.69 | 0.055022 |
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Target: 5'- ---gCAGCAGCUCagugUGCcCCUUCGGGc -3' miRNA: 3'- uaaaGUCGUCGAGg---ACGuGGAGGCUC- -5' |
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| 2210 | 3' | -55.4 | NC_001403.1 | + | 4004 | 0.69 | 0.05121 |
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Target: 5'- ---gCAGCAGCgcaccgcggcccUCC-GCGCCUCCGGc -3' miRNA: 3'- uaaaGUCGUCG------------AGGaCGUGGAGGCUc -5' |
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| 2210 | 3' | -55.4 | NC_001403.1 | + | 2826 | 0.92 | 0.000522 |
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Target: 5'- ---aCAGCGGCUUCUGCACCUCCGGGa -3' miRNA: 3'- uaaaGUCGUCGAGGACGUGGAGGCUC- -5' |
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| 2210 | 3' | -55.4 | NC_001403.1 | + | 2887 | 1.06 | 0.00003 |
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Target: 5'- uAUUUCAGCAGCUCCUGCACCUCCGAGc -3' miRNA: 3'- -UAAAGUCGUCGAGGACGUGGAGGCUC- -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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