miRNA: 3'- gGUCGG------CAACGGAuGUUUCGUCcGGG- -5'
miRNA: 3'- gGUCGGCAACGgAUgUUUCGUc--CGGG- -5'
miRNA: 3'- ggUCGg--CAACGGaugUUUCGUCCGGG- -5'
miRNA: 3'- -GGUCGGCaaCGGAU------GUUUCGUC--CGGG- -5'
miRNA: 3'- -GGUCGGCAACGGAUGUUUCGUCCGGG- -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 | |||||||
| 9405 | 5' | -54.7 | NC_002519.1 | + | 29163 | 0.66 | 0.663198 |
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Target: 5'- aCAGCUgcucuaGUUGCUUuCGGAGUAGaCCCa -3' miRNA: 3'- gGUCGG------CAACGGAuGUUUCGUCcGGG- -5' |
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| 9405 | 5' | -54.7 | NC_002519.1 | + | 18183 | 0.67 | 0.606563 |
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Target: 5'- gCAGCUGUUGCaUGgAGAGCAuuaGCUCa -3' miRNA: 3'- gGUCGGCAACGgAUgUUUCGUc--CGGG- -5' |
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| 9405 | 5' | -54.7 | NC_002519.1 | + | 17329 | 0.7 | 0.424429 |
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Target: 5'- -gGGCaaaGUUGCUg--GAGGCAGGCCUc -3' miRNA: 3'- ggUCGg--CAACGGaugUUUCGUCCGGG- -5' |
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| 9405 | 5' | -54.7 | NC_002519.1 | + | 7700 | 0.7 | 0.386344 |
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Target: 5'- cUCAGCCGcaGCCUGugcaacCAAAGCAGcaGCCUu -3' miRNA: 3'- -GGUCGGCaaCGGAU------GUUUCGUC--CGGG- -5' |
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| 9405 | 5' | -54.7 | NC_002519.1 | + | 31889 | 1.14 | 0.000299 |
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Target: 5'- uCCAGCCGUUGCCUACAAAGCAGGCCCa -3' miRNA: 3'- -GGUCGGCAACGGAUGUUUCGUCCGGG- -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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