miRNA: 3'- uUUAGCUCAGC---------AUGCGGg-----CGGCGGca -5'
miRNA: 3'- -UUUAGCUCa-GCAu-----GCGGGCGGcGGCA- -5'
miRNA: 3'- uuuaGCUCAGCAUGCGGGcGGCGGCA- -5'
miRNA: 3'- uuUAGCUCa----GCaug-CGGGCGGCGGca -5'
miRNA: 3'- -UUUAGCUCAGCAUGCgGGCGGCGGCA- -5'
Results 1 - 5 of 5 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 | |||||||
| 4374 | 5' | -57.8 | NC_001720.1 | + | 13006 | 0.68 | 0.405564 |
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Target: 5'- uGGUCGAGUUGagcaugaaaUACGCCaaguugGCCGCCa- -3' miRNA: 3'- uUUAGCUCAGC---------AUGCGGg-----CGGCGGca -5' |
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| 4374 | 5' | -57.8 | NC_001720.1 | + | 24311 | 0.69 | 0.319796 |
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Target: 5'- gAGGUCGGGacCGUugucuuCGCCCGCC-CCGUg -3' miRNA: 3'- -UUUAGCUCa-GCAu-----GCGGGCGGcGGCA- -5' |
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| 4374 | 5' | -57.8 | NC_001720.1 | + | 6637 | 0.7 | 0.312006 |
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Target: 5'- ---aCGGGUCGUACGUCUcCUGUCGUg -3' miRNA: 3'- uuuaGCUCAGCAUGCGGGcGGCGGCA- -5' |
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| 4374 | 5' | -57.8 | NC_001720.1 | + | 14873 | 0.71 | 0.241998 |
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Target: 5'- -cGUCGGGgucagCGgugaGCCCGCCGCCa- -3' miRNA: 3'- uuUAGCUCa----GCaug-CGGGCGGCGGca -5' |
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| 4374 | 5' | -57.8 | NC_001720.1 | + | 26929 | 0.92 | 0.007549 |
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Target: 5'- gAAAUCGAGUCGUACG-CCGCCGCCGUc -3' miRNA: 3'- -UUUAGCUCAGCAUGCgGGCGGCGGCA- -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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