miRNA: 3'- -GCCGACU-GUCaUAaCUU---------------AGGUAGCGC- -5'
miRNA: 3'- -GCCGa---CUGUCAU-------AACU-UAGGuAGCGc -5'
miRNA: 3'- gCC-GACUGUCAuaaCUUAGGUaGCGc -5'
miRNA: 3'- -GCCGaCUGUCAUAACuuaGGUAGCGc -5'
miRNA: 3'- -GCCGACUGUCAUAACUUAGGUAGCGC- -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 | |||||||
| 23074 | 3' | -49.4 | NC_005178.1 | + | 26400 | 0.67 | 0.873911 |
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Target: 5'- aCGGUUGAcCAG-AUcGAGcagguugccacuaccUCCAUCGCGa -3' miRNA: 3'- -GCCGACU-GUCaUAaCUU---------------AGGUAGCGC- -5' |
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| 23074 | 3' | -49.4 | NC_005178.1 | + | 18073 | 0.67 | 0.861058 |
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Target: 5'- aCGGCgcggGACGGUAgcccuccUUGAcGUCC-UCGCu -3' miRNA: 3'- -GCCGa---CUGUCAU-------AACU-UAGGuAGCGc -5' |
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| 23074 | 3' | -49.4 | NC_005178.1 | + | 17625 | 0.69 | 0.794554 |
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Target: 5'- uGGuCUGACGGUc--GAGUCCAgCGCc -3' miRNA: 3'- gCC-GACUGUCAuaaCUUAGGUaGCGc -5' |
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| 23074 | 3' | -49.4 | NC_005178.1 | + | 13036 | 0.73 | 0.542785 |
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Target: 5'- cCGGC-GACGGUGUUG---CCGUCGCu -3' miRNA: 3'- -GCCGaCUGUCAUAACuuaGGUAGCGc -5' |
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| 23074 | 3' | -49.4 | NC_005178.1 | + | 2320 | 1.1 | 0.002307 |
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Target: 5'- aCGGCUGACAGUAUUGAAUCCAUCGCGc -3' miRNA: 3'- -GCCGACUGUCAUAACUUAGGUAGCGC- -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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