miRNA: 3'- gCGAG-----CCCGCCGCuuCUUGcaaagac -5'
miRNA: 3'- -GCGaGCCCGC-CGC-UUCUUGCaaagac -5'
miRNA: 3'- gCGa-----GCCCGCCGCU---------------UCuuGCAAa-----GAC- -5'
miRNA: 3'- gCGAGCC------------CGCCGCU--UCUUGCaa--AGac -5'
Results 21 - 24 of 24 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 | |||||||
| 26324 | 5' | -54.2 | NC_005345.2 | + | 46368 | 0.66 | 0.743117 |
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Target: 5'- gGCUCacgaaGGGCGGCGgcGAGCa------ -3' miRNA: 3'- gCGAG-----CCCGCCGCuuCUUGcaaagac -5' |
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| 26324 | 5' | -54.2 | NC_005345.2 | + | 18026 | 0.66 | 0.75362 |
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Target: 5'- aCGC-CGGGCGaGCGcAGGAACGc----- -3' miRNA: 3'- -GCGaGCCCGC-CGC-UUCUUGCaaagac -5' |
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| 26324 | 5' | -54.2 | NC_005345.2 | + | 48898 | 0.66 | 0.757786 |
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Target: 5'- gGCgaggugCGGGCGGCGAuggcucccgagaccgAGggUGUUcgaacgCUGc -3' miRNA: 3'- gCGa-----GCCCGCCGCU---------------UCuuGCAAa-----GAC- -5' |
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| 26324 | 5' | -54.2 | NC_005345.2 | + | 4683 | 0.66 | 0.774234 |
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Target: 5'- uGCUCGGcucgacgcccguGCGGCGAacAGGGCGgcgaUCa- -3' miRNA: 3'- gCGAGCC------------CGCCGCU--UCUUGCaa--AGac -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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