miRNA: 3'- cuuUCUUCGU---GAGGU--GCGCGGUaUGa -5'
miRNA: 3'- cuUUCUUCGUGAGGUGCGcg-GUAUga -5'
miRNA: 3'- cuuuCUUCGUGAGG--UG---------------CGCGGUAugA- -5'
miRNA: 3'- cuUUCUucGUGAGGUGCG----CGGUAUGa -5'
miRNA: 3'- -CUUUCUUCGUGAGGUGCGCGGUAUGA- -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 | |||||||
| 22547 | 3' | -51.3 | NC_005083.1 | + | 204227 | 0.67 | 0.995211 |
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Target: 5'- --uAGAAGCAaauUUCCAauUGCGCCAaGCa -3' miRNA: 3'- cuuUCUUCGU---GAGGU--GCGCGGUaUGa -5' |
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| 22547 | 3' | -51.3 | NC_005083.1 | + | 148160 | 0.67 | 0.992613 |
|
Target: 5'- -uGGGAAGCACUUCGCGCugaCGUAa- -3' miRNA: 3'- cuUUCUUCGUGAGGUGCGcg-GUAUga -5' |
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| 22547 | 3' | -51.3 | NC_005083.1 | + | 145596 | 0.67 | 0.991979 |
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Target: 5'- ---uGAAGCACUCCgcGCauguaucgaagcgaaGCGCCGUugUu -3' miRNA: 3'- cuuuCUUCGUGAGG--UG---------------CGCGGUAugA- -5' |
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| 22547 | 3' | -51.3 | NC_005083.1 | + | 76531 | 0.7 | 0.952106 |
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Target: 5'- -uGAGAuuCGCUCCACGCcaauGCCAUAUc -3' miRNA: 3'- cuUUCUucGUGAGGUGCG----CGGUAUGa -5' |
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| 22547 | 3' | -51.3 | NC_005083.1 | + | 119463 | 1.08 | 0.013433 |
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Target: 5'- cGAAAGAAGCACUCCACGCGCCAUACUu -3' miRNA: 3'- -CUUUCUUCGUGAGGUGCGCGGUAUGA- -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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