miRNA: 3'- -UCCCCGGa-CUGCCG-UU---------------CCGGUugCUu -5'
miRNA: 3'- uCCC-CGG----ACUGCCGu-UCCGGU--UGCUu -5'
miRNA: 3'- uCCCCGGaCugCCGuuCCGGU---UG-CUU- -5'
miRNA: 3'- ucCCCGGA--CUGCCGuuCCGGUUGcuu -5'
miRNA: 3'- -UCCCCGGACUGCCGUUCCGGUUGCUU- -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 | |||||||
| 7280 | 5' | -60 | NC_001900.1 | + | 9595 | 0.66 | 0.373784 |
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Target: 5'- uGGGGGUCagGGCGGCuGAucgugauguacgaccGGCCGugGAc -3' miRNA: 3'- -UCCCCGGa-CUGCCG-UU---------------CCGGUugCUu -5' |
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| 7280 | 5' | -60 | NC_001900.1 | + | 25545 | 0.7 | 0.219279 |
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Target: 5'- uGGGaGCCacgcUGGCGGCucAGGCCGguGCGAc -3' miRNA: 3'- uCCC-CGG----ACUGCCGu-UCCGGU--UGCUu -5' |
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| 7280 | 5' | -60 | NC_001900.1 | + | 30776 | 0.7 | 0.202593 |
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Target: 5'- cGGGGCCgGugGGUucGGCCAcucGCuGGAg -3' miRNA: 3'- uCCCCGGaCugCCGuuCCGGU---UG-CUU- -5' |
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| 7280 | 5' | -60 | NC_001900.1 | + | 29825 | 0.71 | 0.177233 |
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Target: 5'- -cGGGUCUacGGCGGUggGGCCAACa-- -3' miRNA: 3'- ucCCCGGA--CUGCCGuuCCGGUUGcuu -5' |
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| 7280 | 5' | -60 | NC_001900.1 | + | 8060 | 1.06 | 0.000411 |
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Target: 5'- cAGGGGCCUGACGGCAAGGCCAACGAAg -3' miRNA: 3'- -UCCCCGGACUGCCGUUCCGGUUGCUU- -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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