miRNA: 3'- -GGUUGUGCugCCG-------------UGGGuu-----CUCCuGu -5'
miRNA: 3'- -GGUUGUgcugCCGUGGGUUCUcCuGU- -5'
miRNA: 3'- -GGUUGUGCUG-------CCGUGGg-------UUCUCCUgu -5'
miRNA: 3'- ggUUGUGCuGCCGuGGGUUCUCCUGu -5'
miRNA: 3'- -GGUUGUGCUGCCGUGGGUUCUCCUGU- -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 | |||||||
| 27488 | 5' | -54.3 | NC_005872.1 | + | 24705 | 0.66 | 0.587613 |
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Target: 5'- gCCAACACGugGGCcacuauggcccuuACCCuagccguGGGGuCc -3' miRNA: 3'- -GGUUGUGCugCCG-------------UGGGuu-----CUCCuGu -5' |
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| 27488 | 5' | -54.3 | NC_005872.1 | + | 13559 | 0.66 | 0.577308 |
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Target: 5'- gCCAACAa---GGCACCCAAGAcGcCAc -3' miRNA: 3'- -GGUUGUgcugCCGUGGGUUCUcCuGU- -5' |
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| 27488 | 5' | -54.3 | NC_005872.1 | + | 13832 | 0.7 | 0.349631 |
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Target: 5'- gCCAACACGGCacccaaaGGCGCCaauguaguGGGAGGAa- -3' miRNA: 3'- -GGUUGUGCUG-------CCGUGGg-------UUCUCCUgu -5' |
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| 27488 | 5' | -54.3 | NC_005872.1 | + | 3258 | 0.73 | 0.242746 |
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Target: 5'- -aAACGCG-CGGCcCCUAAGGGGGCc -3' miRNA: 3'- ggUUGUGCuGCCGuGGGUUCUCCUGu -5' |
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| 27488 | 5' | -54.3 | NC_005872.1 | + | 13652 | 1.1 | 0.000459 |
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Target: 5'- gCCAACACGACGGCACCCAAGAGGACAu -3' miRNA: 3'- -GGUUGUGCUGCCGUGGGUUCUCCUGU- -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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