miRNA: 3'- -GGGUCUa-----UGG-CUCAGgCUaGa-------CCUGG- -5'
miRNA: 3'- -GGGUCUAuGgCUCAGGC-UAGaCCUGG- -5'
miRNA: 3'- -GGGUCuauGGCUCAGGCUagaCCUGG- -5'
miRNA: 3'- -GGGUCUAUGGCUCAGGCUAGACCUGG- -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 | |||||||
| 31276 | 3' | -53.3 | NC_006564.1 | + | 3732 | 0.66 | 0.327786 |
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Target: 5'- uCCCGGAgacagaGCCgGAGUCgGA-CgaggagggGGACCa -3' miRNA: 3'- -GGGUCUa-----UGG-CUCAGgCUaGa-------CCUGG- -5' |
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| 31276 | 3' | -53.3 | NC_006564.1 | + | 3444 | 0.68 | 0.224186 |
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Target: 5'- cUCCGGGU-CgGGGUCCGgGUCgGGAUCc -3' miRNA: 3'- -GGGUCUAuGgCUCAGGC-UAGaCCUGG- -5' |
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| 31276 | 3' | -53.3 | NC_006564.1 | + | 3497 | 0.7 | 0.159537 |
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Target: 5'- aCUCGGuauCUGGGUCCGGgg-GGGCCa -3' miRNA: 3'- -GGGUCuauGGCUCAGGCUagaCCUGG- -5' |
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| 31276 | 3' | -53.3 | NC_006564.1 | + | 3518 | 1.14 | 5.7e-05 |
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Target: 5'- aCCCAGAUACCGAGUCCGAUCUGGACCc -3' miRNA: 3'- -GGGUCUAUGGCUCAGGCUAGACCUGG- -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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