miRNA: 3'- aaCGGCGA---------------CGG--UGAACCAUAGaUCAa -5'
miRNA: 3'- aaCG-GCGACGGUG--------------AACCA--UAGAUCaa -5'
miRNA: 3'- aaCGGCGACGGUGA----ACCA---UAGaUCAa -5'
miRNA: 3'- -AACGGCGACGGUGAACCAUAGAUCAA- -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 | |||||||
| 13126 | 5' | -53.4 | NC_003401.1 | + | 122455 | 0.66 | 0.920126 |
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Target: 5'- -cGCCGCUugaauuucgcgggcgGCUggGCUUGGUGUC-AGUg -3' miRNA: 3'- aaCGGCGA---------------CGG--UGAACCAUAGaUCAa -5' |
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| 13126 | 5' | -53.4 | NC_003401.1 | + | 104878 | 0.66 | 0.915885 |
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Target: 5'- -gGCgCGCUGCCGCgcacgugaaggugaUUGGUcaGUCUGGc- -3' miRNA: 3'- aaCG-GCGACGGUG--------------AACCA--UAGAUCaa -5' |
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| 13126 | 5' | -53.4 | NC_003401.1 | + | 48449 | 0.68 | 0.835433 |
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Target: 5'- -gGCCGUUGCCGCUagauUGGUccgAUCcGGUc -3' miRNA: 3'- aaCGGCGACGGUGA----ACCA---UAGaUCAa -5' |
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| 13126 | 5' | -53.4 | NC_003401.1 | + | 48575 | 1.02 | 0.00805 |
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Target: 5'- cUUGCCGCUGCCACUUGGUAUCUAGUUc -3' miRNA: 3'- -AACGGCGACGGUGAACCAUAGAUCAA- -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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