miRNA: 3'- gaGCGGGGGuCGuCGCuGCUCCu--CCU- -5'
miRNA: 3'- -GAGCGGGGGUCGUCGCUGCUCCUCCU- -5'
miRNA: 3'- gAGCGg----GGGUCGUCG---CUGCUCCUCcu -5'
miRNA: 3'- gaGCGGGGGUCgUCgCUGcuCCUCCU- -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 |
| Predicted miRNA align pattern | |||||||
| 693 | 5' | -61.8 | AC_000018.1 | + | 8194 | 0.66 | 0.288371 |
|
Target: 5'- -cCGCCCCU-GCcGCGcCGAGGucuGGAc -3' miRNA: 3'- gaGCGGGGGuCGuCGCuGCUCCu--CCU- -5' |
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| 693 | 5' | -61.8 | AC_000018.1 | + | 23833 | 1.08 | 0.000146 |
|
Target: 5'- cCUCGCCCCCAGCAGCGACGAGGAGGAg -3' miRNA: 3'- -GAGCGGGGGUCGUCGCUGCUCCUCCU- -5' |
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| 693 | 5' | -61.8 | AC_000018.1 | + | 25661 | 0.66 | 0.26082 |
|
Target: 5'- gUUGCaggguCCCAGCAGUgaaGGCGAGGGGu- -3' miRNA: 3'- gAGCGg----GGGUCGUCG---CUGCUCCUCcu -5' |
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| 693 | 5' | -61.8 | AC_000018.1 | + | 26016 | 0.66 | 0.281276 |
|
Target: 5'- -aCGCCCCCAG-AG-GAUauGGAGGAa -3' miRNA: 3'- gaGCGGGGGUCgUCgCUGcuCCUCCU- -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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