miRNA: 3'- -CGGGCGC----UGCAGUgUGCcAGUGAAGu -5'
miRNA: 3'- -CGGGC-GCUGCAGUGugc-CAGUGa-AGU- -5'
miRNA: 3'- -CGGGCGCUGCagUGuGCCAGUGa-------AGU- -5'
miRNA: 3'- -CGGGCGCUGCaGUGU--GCCaGUGAAGU- -5'
miRNA: 3'- -CGGGCGCUGCAGUGUGCCAGUGAAGU- -5'
Results 21 - 25 of 25 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 | |||||||
| 18967 | 5' | -55.2 | NC_004683.1 | + | 34973 | 0.7 | 0.504291 |
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Target: 5'- aGCCCGUGccgcACGUCAgGCGcUCAUUUCc -3' miRNA: 3'- -CGGGCGC----UGCAGUgUGCcAGUGAAGu -5' |
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| 18967 | 5' | -55.2 | NC_004683.1 | + | 19380 | 0.71 | 0.4839 |
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Target: 5'- uGCCCGcCGACGUCACucacGUCGCgaUCGg -3' miRNA: 3'- -CGGGC-GCUGCAGUGugc-CAGUGa-AGU- -5' |
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| 18967 | 5' | -55.2 | NC_004683.1 | + | 257 | 0.73 | 0.371119 |
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Target: 5'- uGCCCGCGGCGggGC-UGGUCGCgacgguggUCAa -3' miRNA: 3'- -CGGGCGCUGCagUGuGCCAGUGa-------AGU- -5' |
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| 18967 | 5' | -55.2 | NC_004683.1 | + | 40926 | 0.79 | 0.143798 |
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Target: 5'- cGCCCGCGAUG-CACAcuCGG-CACUUCGa -3' miRNA: 3'- -CGGGCGCUGCaGUGU--GCCaGUGAAGU- -5' |
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| 18967 | 5' | -55.2 | NC_004683.1 | + | 54553 | 1.11 | 0.00093 |
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Target: 5'- cGCCCGCGACGUCACACGGUCACUUCAu -3' miRNA: 3'- -CGGGCGCUGCAGUGUGCCAGUGAAGU- -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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