miRNA: 3'- aGGCGGUUCGuGagAGACGgUAGGUg -5'
miRNA: 3'- aggCGGUUCGUGag--AGaCGGUAGGUG- -5'
miRNA: 3'- aGGCGGUUCGUGa-GAGa------CGg--UAGGUG- -5'
miRNA: 3'- aGGCGGUU-CGUGAGAG---ACGGuAGGUG- -5'
miRNA: 3'- -AGGCGGUUCGUGAGAGACGGUAGGUG- -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 | |||||||
| 15502 | 5' | -56.4 | NC_003992.2 | + | 7309 | 0.67 | 0.124816 |
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Target: 5'- aCCGCUGAGC-CaaUCUGCgGUCCGu -3' miRNA: 3'- aGGCGGUUCGuGagAGACGgUAGGUg -5' |
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| 15502 | 5' | -56.4 | NC_003992.2 | + | 6478 | 0.68 | 0.102552 |
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Target: 5'- --gGCCAGGCAUgguaUC-GCCGUCCAUg -3' miRNA: 3'- aggCGGUUCGUGag--AGaCGGUAGGUG- -5' |
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| 15502 | 5' | -56.4 | NC_003992.2 | + | 4617 | 0.69 | 0.086912 |
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Target: 5'- cCCGCCAGGCAUgcCUCaagaacgGCaauGUCCACa -3' miRNA: 3'- aGGCGGUUCGUGa-GAGa------CGg--UAGGUG- -5' |
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| 15502 | 5' | -56.4 | NC_003992.2 | + | 4256 | 0.72 | 0.049079 |
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Target: 5'- aUCGCCGAcGCGCUCUCcagUGUUuUCCACg -3' miRNA: 3'- aGGCGGUU-CGUGAGAG---ACGGuAGGUG- -5' |
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| 15502 | 5' | -56.4 | NC_003992.2 | + | 3707 | 1.09 | 3.6e-05 |
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Target: 5'- uUCCGCCAAGCACUCUCUGCCAUCCACc -3' miRNA: 3'- -AGGCGGUUCGUGAGAGACGGUAGGUG- -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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