miRNA: 3'- aAGGCaCAGCuGGUCCCACGCGaagu -5'
miRNA: 3'- aAGGCAC-AGCU------------GGUCCCaCGCGaaGU- -5'
miRNA: 3'- -AAGGCACAGC-----UGGUCCCa------CGCGAAGu -5'
miRNA: 3'- -AAGGCACAGC-----UGGUCCCa------CGCGAAGu -5'
miRNA: 3'- -AAGGCACAGCUGGUCCCACGCGAAGU- -5'
Results 1 - 5 of 5 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 | |||||||
| 3048 | 5' | -57.2 | NC_001493.1 | + | 111185 | 0.66 | 0.799913 |
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Target: 5'- cUUCG-GUCG-CCGGGGUGUGCc--- -3' miRNA: 3'- aAGGCaCAGCuGGUCCCACGCGaagu -5' |
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| 3048 | 5' | -57.2 | NC_001493.1 | + | 4732 | 0.67 | 0.762588 |
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Target: 5'- cUCCGUGuUCGGguuugggcacacCCGGGG-GCGCggCAg -3' miRNA: 3'- aAGGCAC-AGCU------------GGUCCCaCGCGaaGU- -5' |
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| 3048 | 5' | -57.2 | NC_001493.1 | + | 14591 | 0.68 | 0.713348 |
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Target: 5'- uUUCCGUGUUGuuucuGCCAGGGggaggccGUGUUUCc -3' miRNA: 3'- -AAGGCACAGC-----UGGUCCCa------CGCGAAGu -5' |
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| 3048 | 5' | -57.2 | NC_001493.1 | + | 130145 | 0.68 | 0.713348 |
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Target: 5'- uUUCCGUGUUGuuucuGCCAGGGggaggccGUGUUUCc -3' miRNA: 3'- -AAGGCACAGC-----UGGUCCCa------CGCGAAGu -5' |
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| 3048 | 5' | -57.2 | NC_001493.1 | + | 28527 | 1.06 | 0.002886 |
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Target: 5'- uUUCCGUGUCGACCAGGGUGCGCUUCAc -3' miRNA: 3'- -AAGGCACAGCUGGUCCCACGCGAAGU- -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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