miRNA: 3'- ccGGGGACGGUUGU------CGUCuUGGUCGC- -5'
miRNA: 3'- cCGGGG-----------ACGGUUGUCGuCUUGgu-CGc -5'
miRNA: 3'- -CCGGg------------GACGGU--UGUCGUCUUGGUCgC- -5'
miRNA: 3'- -CCGGGGACGGUUGUCGUCUUGGUCGC- -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 | |||||||
| 22227 | 5' | -57.9 | NC_005039.1 | + | 7592 | 0.67 | 0.151557 |
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Target: 5'- -aCCCCUGUCAAUAaugguuGCAG-GCUGGCGg -3' miRNA: 3'- ccGGGGACGGUUGU------CGUCuUGGUCGC- -5' |
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| 22227 | 5' | -57.9 | NC_005039.1 | + | 3981 | 0.67 | 0.138131 |
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Target: 5'- uGCCCUcuacacaugcaUGCCGACAGCuGGACaauGCu -3' miRNA: 3'- cCGGGG-----------ACGGUUGUCGuCUUGgu-CGc -5' |
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| 22227 | 5' | -57.9 | NC_005039.1 | + | 7246 | 0.74 | 0.034186 |
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Target: 5'- gGGCCaucaacaaccucaCUGCCAucACAGCAGGACUAGgGu -3' miRNA: 3'- -CCGGg------------GACGGU--UGUCGUCUUGGUCgC- -5' |
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| 22227 | 5' | -57.9 | NC_005039.1 | + | 7261 | 1.11 | 0.000029 |
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Target: 5'- uGGCCCCUGCCAACAGCAGAACCAGCGg -3' miRNA: 3'- -CCGGGGACGGUUGUCGUCUUGGUCGC- -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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