miRNA: 3'- -GGCgCGGaa--GGUAGGCCGCgUCUUAa -5'
miRNA: 3'- -GGCGCGGaAGgUAGGCCG-----------CGUCUuaa -5'
miRNA: 3'- -GGC-GC-GGa--AGGUAGGCCGCGUCUUaa -5'
miRNA: 3'- -GGCGCGgAAGGuAGGCCGCGU---CUUAa -5'
miRNA: 3'- -GGCGCGGAAGGUAGGCCGCGUCUUAA- -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 | |||||||
| 12660 | 3' | -56.6 | NC_003345.1 | + | 71041 | 0.66 | 0.744016 |
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Target: 5'- uUCGgGCUgucgUCGUCCGGUGgGGAAUc -3' miRNA: 3'- -GGCgCGGaa--GGUAGGCCGCgUCUUAa -5' |
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| 12660 | 3' | -56.6 | NC_003345.1 | + | 62306 | 0.66 | 0.7338 |
|
Target: 5'- gCCGCGCUcUCaAUCCGGUcaacguuagaaGCAGAc-- -3' miRNA: 3'- -GGCGCGGaAGgUAGGCCG-----------CGUCUuaa -5' |
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| 12660 | 3' | -56.6 | NC_003345.1 | + | 8068 | 0.68 | 0.574681 |
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Target: 5'- cCCGaCGaCCcggUUCAUCCGGUGUGGAAg- -3' miRNA: 3'- -GGC-GC-GGa--AGGUAGGCCGCGUCUUaa -5' |
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| 12660 | 3' | -56.6 | NC_003345.1 | + | 39992 | 0.7 | 0.502014 |
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Target: 5'- uCUGUGCgUUCC-UCCGGCGUAcacGAGUa -3' miRNA: 3'- -GGCGCGgAAGGuAGGCCGCGU---CUUAa -5' |
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| 12660 | 3' | -56.6 | NC_003345.1 | + | 60609 | 1.07 | 0.001579 |
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Target: 5'- cCCGCGCCUUCCAUCCGGCGCAGAAUUu -3' miRNA: 3'- -GGCGCGGAAGGUAGGCCGCGUCUUAA- -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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