miRNA: 3'- caCGGCUCGGCG--------CGCGc-CCGU-CUUCa -5'
miRNA: 3'- caCGGcUCGGCGCGC----GC-CCguCUUCA- -5'
miRNA: 3'- caCG-GCUcGGCg----CGCGCCCGUCUUca -5'
miRNA: 3'- caCGGCU----CGGCGcGCGCcCGUCUUCa -5'
miRNA: 3'- -CACGGCUCGGCGCGCGCCCGUCUUCA- -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 | |||||||
| 8833 | 3' | -62.5 | NC_002484.1 | + | 41685 | 0.66 | 0.351662 |
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Target: 5'- -gGCCGAGCUGCucgccgccGCGCccGGCAaGGAGg -3' miRNA: 3'- caCGGCUCGGCG--------CGCGc-CCGU-CUUCa -5' |
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| 8833 | 3' | -62.5 | NC_002484.1 | + | 30364 | 0.66 | 0.33576 |
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Target: 5'- -aGCC-AGCCGCGCGgcucUGaGGguGGAGUu -3' miRNA: 3'- caCGGcUCGGCGCGC----GC-CCguCUUCA- -5' |
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| 8833 | 3' | -62.5 | NC_002484.1 | + | 26044 | 0.66 | 0.328008 |
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Target: 5'- -aGCgCGA-CCGauaaaGCGCGGGCGGAGa- -3' miRNA: 3'- caCG-GCUcGGCg----CGCGCCCGUCUUca -5' |
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| 8833 | 3' | -62.5 | NC_002484.1 | + | 36995 | 0.71 | 0.158509 |
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Target: 5'- -cGCCGAagcuGCCGCcCGCGaGCAGAAGg -3' miRNA: 3'- caCGGCU----CGGCGcGCGCcCGUCUUCa -5' |
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| 8833 | 3' | -62.5 | NC_002484.1 | + | 27729 | 1.06 | 0.000335 |
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Target: 5'- uGUGCCGAGCCGCGCGCGGGCAGAAGUu -3' miRNA: 3'- -CACGGCUCGGCGCGCGCCCGUCUUCA- -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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