miRNA: 3'- ggcCUGCG----CGCGCGGUGCACg--CUCCG- -5'
miRNA: 3'- -GGC-CUGcGCGCGcgGUGCACGC---UCCG- -5'
miRNA: 3'- -GGcCUGCgCgc-GcgGUGCACGCUCCG- -5'
miRNA: 3'- ggCCU---GCGCGcGCGGUGCACGCU-CCg -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 | |||||||
| 1200 | 3' | -61.9 | NC_001132.2 | + | 7473 | 0.66 | 0.69475 |
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Target: 5'- --cGACGUcuacGCGCGUUACGUGgaaGAGGUa -3' miRNA: 3'- ggcCUGCG----CGCGCGGUGCACg--CUCCG- -5' |
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| 1200 | 3' | -61.9 | NC_001132.2 | + | 134098 | 0.66 | 0.685235 |
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Target: 5'- cUCGuGAC-CGCGUuaCACGUGUGccaGGGCg -3' miRNA: 3'- -GGC-CUGcGCGCGcgGUGCACGC---UCCG- -5' |
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| 1200 | 3' | -61.9 | NC_001132.2 | + | 121712 | 0.67 | 0.627578 |
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Target: 5'- aCCuGACGgGgaaCuaCACGUGCGAGGCg -3' miRNA: 3'- -GGcCUGCgCgc-GcgGUGCACGCUCCG- -5' |
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| 1200 | 3' | -61.9 | NC_001132.2 | + | 41446 | 0.74 | 0.286273 |
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Target: 5'- -aGGAaccCGCGCaCGCCACGUGCGGuGGg -3' miRNA: 3'- ggCCU---GCGCGcGCGGUGCACGCU-CCg -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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