miRNA: 3'- uCUUGGUGCuUGC-GUAGCGCUGGGac -5'
miRNA: 3'- -UCUug--GUGCUUGCG-------UAGCGCUGGGac -5'
miRNA: 3'- ucuUGGUGCUUgCG-UAGCGCUGGGAC- -5'
miRNA: 3'- uCUUGG-------UGCU---UGCGUAGCGCUGGGAC- -5'
miRNA: 3'- -UCUUGGUGCUUGCGUAGCGCUGGGAC- -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 | |||||||
| 1395 | 3' | -54.4 | NC_001335.1 | + | 8248 | 0.71 | 0.446382 |
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Target: 5'- cGAACUACG-ACGcCAUCGCGAUUCg- -3' miRNA: 3'- uCUUGGUGCuUGC-GUAGCGCUGGGac -5' |
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| 1395 | 3' | -54.4 | NC_001335.1 | + | 13488 | 0.73 | 0.362006 |
|
Target: 5'- aAGGucuaCGCGAACGCgaacaagGUCGCGGCCCg- -3' miRNA: 3'- -UCUug--GUGCUUGCG-------UAGCGCUGGGac -5' |
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| 1395 | 3' | -54.4 | NC_001335.1 | + | 11786 | 0.75 | 0.283564 |
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Target: 5'- --cAUCGCGAAgGCgGUCGCGACCUUGg -3' miRNA: 3'- ucuUGGUGCUUgCG-UAGCGCUGGGAC- -5' |
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| 1395 | 3' | -54.4 | NC_001335.1 | + | 39096 | 0.78 | 0.185553 |
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Target: 5'- uGAACUcucggugAUGAguaGCGCAUCGUGGCCCUGg -3' miRNA: 3'- uCUUGG-------UGCU---UGCGUAGCGCUGGGAC- -5' |
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| 1395 | 3' | -54.4 | NC_001335.1 | + | 37447 | 1.08 | 0.001381 |
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Target: 5'- gAGAACCACGAACGCAUCGCGACCCUGu -3' miRNA: 3'- -UCUUGGUGCUUGCGUAGCGCUGGGAC- -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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