miRNA: 3'- gUGGGAG------------UGGGAgUUGUGCG----------UUCCGg -5'
miRNA: 3'- guGGGAg--UGGGaGUUGugC-GUUCCGG- -5'
miRNA: 3'- gUGGGAG-UGGga--GUUGUGCgu--UCCGg -5'
miRNA: 3'- -GUGGGAgUGGGAGUUGUGCgu--------UCCGG- -5'
Results 21 - 24 of 24 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 | |||||||
| 4377 | 3' | -56.1 | NC_001720.1 | + | 18722 | 0.66 | 0.594478 |
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Target: 5'- gGCCCUCcgcuuuuccacgGCCUUgAGCGCGUccucgccgugGAGGCg -3' miRNA: 3'- gUGGGAG------------UGGGAgUUGUGCG----------UUCCGg -5' |
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| 4377 | 3' | -56.1 | NC_001720.1 | + | 37661 | 0.66 | 0.594478 |
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Target: 5'- -gUCCUggaACCUgCAGCugGuCGAGGCCa -3' miRNA: 3'- guGGGAg--UGGGaGUUGugC-GUUCCGG- -5' |
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| 4377 | 3' | -56.1 | NC_001720.1 | + | 7295 | 0.66 | 0.605587 |
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Target: 5'- gGCCCUCgACCagccCAGCACGaagcAGGCg -3' miRNA: 3'- gUGGGAG-UGGga--GUUGUGCgu--UCCGg -5' |
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| 4377 | 3' | -56.1 | NC_001720.1 | + | 16265 | 0.66 | 0.605587 |
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Target: 5'- gCAUCCU-GCCCUCAGUGCGaccuaccauuAGGCCg -3' miRNA: 3'- -GUGGGAgUGGGAGUUGUGCgu--------UCCGG- -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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