miRNA: 3'- gUCACC-GUCUUC--------------CGu-----AGCGUCCGCAa -5'
miRNA: 3'- gucACCGUCUUCCGUaGCGU-----CCGCaa -5'
miRNA: 3'- gUCAC-CGUCu---UCCGUAGCGuCCGCAA- -5'
miRNA: 3'- -GUCACCGUCUUCCGUAGCGUCCGCAA- -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 | |||||||
| 13573 | 3' | -56.9 | NC_003444.1 | + | 29977 | 0.67 | 0.406735 |
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Target: 5'- uGGUGGcCGGAAGaugcagaucauauuGCuuuuauUCGCGGGCGUa -3' miRNA: 3'- gUCACC-GUCUUC--------------CGu-----AGCGUCCGCAa -5' |
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| 13573 | 3' | -56.9 | NC_003444.1 | + | 4167 | 0.69 | 0.304125 |
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Target: 5'- --aUGGCAGGAGGCG-CGCAacagcGGCGc- -3' miRNA: 3'- gucACCGUCUUCCGUaGCGU-----CCGCaa -5' |
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| 13573 | 3' | -56.9 | NC_003444.1 | + | 27163 | 0.7 | 0.259736 |
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Target: 5'- gAGUGuGCAGcuccGGGCGUCGU-GGCGUUu -3' miRNA: 3'- gUCAC-CGUCu---UCCGUAGCGuCCGCAA- -5' |
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| 13573 | 3' | -56.9 | NC_003444.1 | + | 3114 | 1.05 | 0.000572 |
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Target: 5'- uCAGUGGCAGAAGGCAUCGCAGGCGUUa -3' miRNA: 3'- -GUCACCGUCUUCCGUAGCGUCCGCAA- -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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