miRNA: 3'- -CUuuCCUUGGGGG------UCGUUGacc-UUCC- -5'
miRNA: 3'- -CuuUCCUUGGGGG--------------UCGUUGACCUu---CC- -5'
miRNA: 3'- -CUUUCCUUGG-GGGUCGuUGACCuuCc -5'
miRNA: 3'- -CUUUCCUUGGGGGUCGUUGACCUUCC- -5'
Results 1 - 4 of 4 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 | |||||||
| 3143 | 3' | -52.3 | NC_001498.1 | + | 8969 | 0.66 | 0.504812 |
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Target: 5'- cGAuuGGGACCCCCuuuauaGGCAACcuaaAAGGa -3' miRNA: 3'- -CUuuCCUUGGGGG------UCGUUGacc-UUCC- -5' |
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| 3143 | 3' | -52.3 | NC_001498.1 | + | 5075 | 0.76 | 0.117747 |
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Target: 5'- uGggGGGGGCCCCCcgucuuggauugucGGUGGCUGGGugcuGGg -3' miRNA: 3'- -CuuUCCUUGGGGG--------------UCGUUGACCUu---CC- -5' |
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| 3143 | 3' | -52.3 | NC_001498.1 | + | 4769 | 0.76 | 0.111586 |
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Target: 5'- gGGGAGGGGCCuUCCAGUuGCUGGggGu -3' miRNA: 3'- -CUUUCCUUGG-GGGUCGuUGACCuuCc -5' |
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| 3143 | 3' | -52.3 | NC_001498.1 | + | 4719 | 1.1 | 0.000308 |
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Target: 5'- gGAAAGGAACCCCCAGCAACUGGAAGGc -3' miRNA: 3'- -CUUUCCUUGGGGGUCGUUGACCUUCC- -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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