miRNA: 3'- -UACGGCUGGUUU---------UGCCaGugGAACGA- -5'
miRNA: 3'- -UACG-GcuGGUUUUGC-CAGUGGAACGa -5'
miRNA: 3'- uaCggCUGGUUuUGCCaGUGGAACGa -5'
miRNA: 3'- -UACGGCUGGUUUUGCCAGUGGAACGA- -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 | |||||||
| 3504 | 5' | -53 | NC_001623.1 | + | 105420 | 0.71 | 0.762244 |
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Target: 5'- uAUGUCGACCGAAauaaauuggGCGGcCugUUUGCUu -3' miRNA: 3'- -UACGGCUGGUUU---------UGCCaGugGAACGA- -5' |
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| 3504 | 5' | -53 | NC_001623.1 | + | 25547 | 0.71 | 0.742177 |
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Target: 5'- uAUGCgCuuCCAAAACGuGUCAUCUUGCa -3' miRNA: 3'- -UACG-GcuGGUUUUGC-CAGUGGAACGa -5' |
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| 3504 | 5' | -53 | NC_001623.1 | + | 114529 | 0.72 | 0.711317 |
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Target: 5'- -aGuuGACCAAcGCGGaCGCUUUGCa -3' miRNA: 3'- uaCggCUGGUUuUGCCaGUGGAACGa -5' |
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| 3504 | 5' | -53 | NC_001623.1 | + | 25867 | 1.05 | 0.007056 |
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Target: 5'- cAUGCCGACCAAAACGGUCACCUUGCUu -3' miRNA: 3'- -UACGGCUGGUUUUGCCAGUGGAACGA- -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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