miRNA: 3'- gCGCGAa----GGCCCU--AUCC--------ACGUAgCGU- -5'
miRNA: 3'- gCGCGaa---GGCCCUAUccaCGUAGCGU- -5'
miRNA: 3'- gCGCgaAgGCCCU--AUCCACGuAGCGU- -5'
miRNA: 3'- -GCGCGAAGGCCCUAUCCACGUAGCGU- -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 | |||||||
| 1270 | 5' | -56.5 | NC_001317.1 | + | 18688 | 0.67 | 0.430097 |
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Target: 5'- uGUGCUgguugCCGGGAugUAGGaauuacccUGCGUgGCGc -3' miRNA: 3'- gCGCGAa----GGCCCU--AUCC--------ACGUAgCGU- -5' |
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| 1270 | 5' | -56.5 | NC_001317.1 | + | 3621 | 0.69 | 0.329366 |
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Target: 5'- aGCGCgacggCUGGGAUG---GCAUCGCAc -3' miRNA: 3'- gCGCGaa---GGCCCUAUccaCGUAGCGU- -5' |
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| 1270 | 5' | -56.5 | NC_001317.1 | + | 953 | 0.72 | 0.198617 |
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Target: 5'- aGCGggUgCGGGAugUAGGUGC-UCGCGa -3' miRNA: 3'- gCGCgaAgGCCCU--AUCCACGuAGCGU- -5' |
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| 1270 | 5' | -56.5 | NC_001317.1 | + | 24808 | 1.08 | 0.000368 |
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Target: 5'- gCGCGCUUCCGGGAUAGGUGCAUCGCAu -3' miRNA: 3'- -GCGCGAAGGCCCUAUCCACGUAGCGU- -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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