miRNA: 3'- uCGagCGGU--------UCGA-GUUGCCGCACuUG- -5'
miRNA: 3'- uCGAGCGGUU---CGAGU--------UGCCG-CAC---UUG- -5'
miRNA: 3'- -UCG-AGCGGUU-CG-----AGUUGCCGCaCUUG- -5'
miRNA: 3'- -UCGAGCGGUUCGAGUUGCCGCACUUG- -5'
Results 21 - 24 of 24 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 | |||||||
| 11952 | 3' | -54.7 | NC_003278.1 | + | 23038 | 0.7 | 0.344444 |
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Target: 5'- uGCagGCCGaccgcgacAGCUaCGACGGCGUGcGCg -3' miRNA: 3'- uCGagCGGU--------UCGA-GUUGCCGCACuUG- -5' |
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| 11952 | 3' | -54.7 | NC_003278.1 | + | 5082 | 0.71 | 0.319102 |
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Target: 5'- uGCUCGCCGAguuGCUCAcccaggucGCGGCuGUGcucGGCg -3' miRNA: 3'- uCGAGCGGUU---CGAGU--------UGCCG-CAC---UUG- -5' |
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| 11952 | 3' | -54.7 | NC_003278.1 | + | 13186 | 0.73 | 0.238281 |
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Target: 5'- aGGCaUCGCCGAcGCgaccgUCGGCGGCGcGGGCg -3' miRNA: 3'- -UCG-AGCGGUU-CG-----AGUUGCCGCaCUUG- -5' |
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| 11952 | 3' | -54.7 | NC_003278.1 | + | 5279 | 1.09 | 0.000513 |
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Target: 5'- cAGCUCGCCAAGCUCAACGGCGUGAACu -3' miRNA: 3'- -UCGAGCGGUUCGAGUUGCCGCACUUG- -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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