miRNA: 3'- gGGCGcCGCGUGUG-----------ACGC-CACA----------CCCA- -5'
miRNA: 3'- gGGC-GCCGCGUGugacGCCACACCCa -5'
miRNA: 3'- gGGCGCCGCguGugACGCCAcACCCa -5'
miRNA: 3'- -GGGCGCCGCGUGUGACGCCACACCCA- -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 | |||||||
| 30586 | 3' | -61.9 | NC_006549.1 | + | 72518 | 0.66 | 0.663749 |
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Target: 5'- aCCGCcGCGCGCGCcacguuucccaUGCGcGUGUuuaaagcguuGGGUg -3' miRNA: 3'- gGGCGcCGCGUGUG-----------ACGC-CACA----------CCCA- -5' |
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| 30586 | 3' | -61.9 | NC_006549.1 | + | 5299 | 0.66 | 0.614533 |
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Target: 5'- gUCGuCGGCGCGC----UGGUGUGGGg -3' miRNA: 3'- gGGC-GCCGCGUGugacGCCACACCCa -5' |
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| 30586 | 3' | -61.9 | NC_006549.1 | + | 70627 | 0.67 | 0.594884 |
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Target: 5'- gCCGUGGCG--UugUGCGGUuUGGGc -3' miRNA: 3'- gGGCGCCGCguGugACGCCAcACCCa -5' |
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| 30586 | 3' | -61.9 | NC_006549.1 | + | 33156 | 1.09 | 0.00081 |
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Target: 5'- aCCCGCGGCGCACACUGCGGUGUGGGUg -3' miRNA: 3'- -GGGCGCCGCGUGUGACGCCACACCCA- -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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