miRNA: 3'- -GGA-CGCAUAgaaGCGCa--CU-CUUGGCC- -5'
miRNA: 3'- -GGACGCAuaGa--------AGCGCACUCUUGG----CC- -5'
miRNA: 3'- gGACGCAU-AGaa----GCGCACUCUUGgCC- -5'
miRNA: 3'- -GGACGCa-UAGaaGCGCaCUCUUGGCC- -5'
miRNA: 3'- -GGACGCAUAGAAGCGCACUCUUGGCC- -5'
Results 21 - 25 of 25 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 | |||||||
| 16041 | 3' | -51.2 | NC_004065.1 | + | 100350 | 0.71 | 0.965143 |
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Target: 5'- cCCUgGCGUAUag-CGCGgaaGAuGAGCCGGu -3' miRNA: 3'- -GGA-CGCAUAgaaGCGCa--CU-CUUGGCC- -5' |
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| 16041 | 3' | -51.2 | NC_004065.1 | + | 123194 | 0.71 | 0.9583 |
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Target: 5'- gCCUGCGUcgUgcccgugugUUGCGUGAGGGCUuccuGGa -3' miRNA: 3'- -GGACGCAuaGa--------AGCGCACUCUUGG----CC- -5' |
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| 16041 | 3' | -51.2 | NC_004065.1 | + | 165524 | 0.72 | 0.95059 |
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Target: 5'- gUUGCGUGcUCcuugagCGCGUGGGGACgGGu -3' miRNA: 3'- gGACGCAU-AGaa----GCGCACUCUUGgCC- -5' |
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| 16041 | 3' | -51.2 | NC_004065.1 | + | 129611 | 0.76 | 0.789192 |
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Target: 5'- uUCUGCGcgGUCagCGCG-GAGAACUGGa -3' miRNA: 3'- -GGACGCa-UAGaaGCGCaCUCUUGGCC- -5' |
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| 16041 | 3' | -51.2 | NC_004065.1 | + | 75711 | 1.14 | 0.007991 |
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Target: 5'- uCCUGCGUAUCUUCGCGUGAGAACCGGg -3' miRNA: 3'- -GGACGCAUAGAAGCGCACUCUUGGCC- -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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