miRNA: 3'- -GCUCGCAAA--UAGUUU------------UAC-CGCGGCcg -5'
miRNA: 3'- gCUCg-CAAauagUUUUACCGCgGCCG- -5'
miRNA: 3'- gcUCGCaaauAGUUUUACCG--CG-GCCG- -5'
miRNA: 3'- -GCUCGCaaauaGUUUU-------------ACCGCGGCcg -5'
miRNA: 3'- -GCUCGCAAAUAGUUUUACCGCGGCCG- -5'
Results 21 - 25 of 25 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 | |||||||
| 22873 | 3' | -49.1 | NC_005137.2 | + | 116340 | 0.67 | 0.996014 |
|
Target: 5'- aCGGGCGUUUacGUCAAGcuuaaacgauuuGUGcGCGCUGa- -3' miRNA: 3'- -GCUCGCAAA--UAGUUU------------UAC-CGCGGCcg -5' |
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| 22873 | 3' | -49.1 | NC_005137.2 | + | 1334 | 0.66 | 0.997605 |
|
Target: 5'- gGAGgaGUUa---AAGGUGGCGgCGGCg -3' miRNA: 3'- gCUCg-CAAauagUUUUACCGCgGCCG- -5' |
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| 22873 | 3' | -49.1 | NC_005137.2 | + | 82948 | 0.66 | 0.998 |
|
Target: 5'- -aAGCG----UCGAGAUGGCacGCgCGGCa -3' miRNA: 3'- gcUCGCaaauAGUUUUACCG--CG-GCCG- -5' |
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| 22873 | 3' | -49.1 | NC_005137.2 | + | 67725 | 0.65 | 0.998307 |
|
Target: 5'- gCGAGCGacgg-CGAGAccguguuggaguuUGGCGCCGa- -3' miRNA: 3'- -GCUCGCaaauaGUUUU-------------ACCGCGGCcg -5' |
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| 22873 | 3' | -49.1 | NC_005137.2 | + | 95429 | 1.15 | 0.005197 |
|
Target: 5'- aCGAGCGUUUAUCAAAAUGGCGCCGGCg -3' miRNA: 3'- -GCUCGCAAAUAGUUUUACCGCGGCCG- -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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