miRNA: 3'- -CUUCa---GAGUC-AC-AGACUUgAUGUCGG- -5'
miRNA: 3'- -CUUCAGAGUCacagaCUUGAUGUCGg -5'
miRNA: 3'- cuUCAGa--GUCACAGaCUUGAU-GUCGG- -5'
miRNA: 3'- -CUUCAGAGUCACAGACUUGAUGUCGG- -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 | |||||||
| 18208 | 3' | -48.5 | NC_004680.1 | + | 39129 | 0.66 | 0.976138 |
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Target: 5'- gGAAGacgaCUCGGcUGcUUUGGAgUGCGGCCa -3' miRNA: 3'- -CUUCa---GAGUC-AC-AGACUUgAUGUCGG- -5' |
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| 18208 | 3' | -48.5 | NC_004680.1 | + | 24621 | 0.68 | 0.934708 |
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Target: 5'- cGAGGUCUCGGcg---GGGCUGCGGUa -3' miRNA: 3'- -CUUCAGAGUCacagaCUUGAUGUCGg -5' |
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| 18208 | 3' | -48.5 | NC_004680.1 | + | 44434 | 0.71 | 0.798144 |
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Target: 5'- -uGGUUguaCGGUGUC-GAACUGcCAGCCg -3' miRNA: 3'- cuUCAGa--GUCACAGaCUUGAU-GUCGG- -5' |
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| 18208 | 3' | -48.5 | NC_004680.1 | + | 36097 | 1.13 | 0.002902 |
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Target: 5'- gGAAGUCUCAGUGUCUGAACUACAGCCu -3' miRNA: 3'- -CUUCAGAGUCACAGACUUGAUGUCGG- -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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