miRNA: 3'- cuCGCACGAGCGCGACu--GGCuagGCU- -5'
miRNA: 3'- -CUCGCACGAGCGCGacugGCUAGGcu -5'
miRNA: 3'- cuCGCACGAGCGCG-------------ACUGGCUa-------GGCU- -5'
miRNA: 3'- -CUCGCACGAgCGCGACUGGCua--G-GCU- -5'
miRNA: 3'- -CUCGCACGAGCGCGACUGGCUAGGCU- -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 | |||||||
| 8562 | 3' | -58.3 | NC_002169.1 | + | 64412 | 0.66 | 0.787531 |
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Target: 5'- -uGCGUGCUCGUGCUGuggUCGua-CGGc -3' miRNA: 3'- cuCGCACGAGCGCGACu--GGCuagGCU- -5' |
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| 8562 | 3' | -58.3 | NC_002169.1 | + | 106497 | 0.68 | 0.70132 |
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Target: 5'- cGGGCGUGUUCGCGCca--CGGUUCa- -3' miRNA: 3'- -CUCGCACGAGCGCGacugGCUAGGcu -5' |
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| 8562 | 3' | -58.3 | NC_002169.1 | + | 36923 | 0.68 | 0.67022 |
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Target: 5'- -uGCGUGUUCGUGCgaggucggcuacgUGGCCGAcuucaacgCCGAc -3' miRNA: 3'- cuCGCACGAGCGCG-------------ACUGGCUa-------GGCU- -5' |
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| 8562 | 3' | -58.3 | NC_002169.1 | + | 80016 | 0.73 | 0.385036 |
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Target: 5'- uGGGCGUGUUgGUGCUGACCGccugCgCGAu -3' miRNA: 3'- -CUCGCACGAgCGCGACUGGCua--G-GCU- -5' |
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| 8562 | 3' | -58.3 | NC_002169.1 | + | 73636 | 1.08 | 0.001897 |
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Target: 5'- uGAGCGUGCUCGCGCUGACCGAUCCGAc -3' miRNA: 3'- -CUCGCACGAGCGCGACUGGCUAGGCU- -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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