miRNA: 3'- ugCGGUa--GGAGGCU--ACCGAGGCUCCU- -5'
miRNA: 3'- -UGCGGU-------------AGGAGGCUA------CCGAGGcUCCU- -5'
miRNA: 3'- uGCGGUAGGa--------GGCuaCCGAGGCUCcu -5'
miRNA: 3'- -UGCGGUAGGAGGCUACCGAGGCUCCU- -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 | |||||||
| 4323 | 3' | -59.1 | NC_001720.1 | + | 7385 | 0.66 | 0.443307 |
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Target: 5'- -gGUUAgggCUUCUGGugUGGCUUCGAGGAg -3' miRNA: 3'- ugCGGUa--GGAGGCU--ACCGAGGCUCCU- -5' |
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| 4323 | 3' | -59.1 | NC_001720.1 | + | 26266 | 0.68 | 0.335764 |
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Target: 5'- gGCGCUGucuccgcucuauuUCCUCCGGUgguauaGGCUCCaGGGGc -3' miRNA: 3'- -UGCGGU-------------AGGAGGCUA------CCGAGGcUCCU- -5' |
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| 4323 | 3' | -59.1 | NC_001720.1 | + | 26516 | 0.71 | 0.213838 |
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Target: 5'- uCGCCGUCCgccucggaaCCGccGGCUCCGAGc- -3' miRNA: 3'- uGCGGUAGGa--------GGCuaCCGAGGCUCcu -5' |
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| 4323 | 3' | -59.1 | NC_001720.1 | + | 4112 | 1.08 | 0.000363 |
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Target: 5'- aACGCCAUCCUCCGAUGGCUCCGAGGAg -3' miRNA: 3'- -UGCGGUAGGAGGCUACCGAGGCUCCU- -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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