miRNA: 3'- -AG-GUCGCAUA-------GCGUa-UCG-AGGGCGAa -5'
miRNA: 3'- -AGGu---CG-CAUa----GCG----UAUCGAGGGCGAa -5'
miRNA: 3'- -AGGu--CGCaUAGCGUaUCGa--GGGCGAa -5'
miRNA: 3'- aGGUCgCa------UAGCGUAUCGAGgGCGAa -5'
miRNA: 3'- -AGGUCGCAUAGCGUAUCGAGGGCGAA- -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 | |||||||
| 13407 | 5' | -55.5 | NC_003409.1 | + | 40019 | 0.66 | 0.889385 |
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Target: 5'- uUCgCGGCGUGUauggggaCGCGacGGCaUCCCGCUg -3' miRNA: 3'- -AG-GUCGCAUA-------GCGUa-UCG-AGGGCGAa -5' |
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| 13407 | 5' | -55.5 | NC_003409.1 | + | 125379 | 0.67 | 0.852508 |
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Target: 5'- aUCCugcuGCuGUGgcuccCGCugcuGUGGCUCCCGCUg -3' miRNA: 3'- -AGGu---CG-CAUa----GCG----UAUCGAGGGCGAa -5' |
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| 13407 | 5' | -55.5 | NC_003409.1 | + | 110322 | 0.67 | 0.818629 |
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Target: 5'- aUCCcucGCG-AUCGCAaAGCggaCCCGCUa -3' miRNA: 3'- -AGGu--CGCaUAGCGUaUCGa--GGGCGAa -5' |
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| 13407 | 5' | -55.5 | NC_003409.1 | + | 120144 | 0.68 | 0.781895 |
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Target: 5'- gCCAGgGgaccaagGUCGUAUGGUUCgCGCUa -3' miRNA: 3'- aGGUCgCa------UAGCGUAUCGAGgGCGAa -5' |
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| 13407 | 5' | -55.5 | NC_003409.1 | + | 84151 | 1.06 | 0.003452 |
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Target: 5'- gUCCAGCGUAUCGCAUAGCUCCCGCUUg -3' miRNA: 3'- -AGGUCGCAUAGCGUAUCGAGGGCGAA- -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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