miRNA: 3'- -UCGCUGgGGCUGCUGuaCGa--------------CGCGcu -5'
miRNA: 3'- -UCGCU---GGGGC----------UGCUGUacGACGCGCU- -5'
miRNA: 3'- uCGc---UG-GGGCUGCuGuACGACGCGCU- -5'
miRNA: 3'- uCGCUGGgGCUGC----UGUACGACGCGCU- -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 | |||||||
| 20881 | 3' | -59.1 | NC_004689.1 | + | 16998 | 0.66 | 0.572669 |
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Target: 5'- cGGUGGCaCCGACGACcgGCguccagagaagcuggGCGCu- -3' miRNA: 3'- -UCGCUGgGGCUGCUGuaCGa--------------CGCGcu -5' |
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| 20881 | 3' | -59.1 | NC_004689.1 | + | 22821 | 0.66 | 0.561255 |
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Target: 5'- aAGCGAgacCCCCGgcugccucccACGACGa-CUGUGCGAa -3' miRNA: 3'- -UCGCU---GGGGC----------UGCUGUacGACGCGCU- -5' |
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| 20881 | 3' | -59.1 | NC_004689.1 | + | 68936 | 0.66 | 0.561255 |
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Target: 5'- uGCacuuACaCCCGGCGuC-UGCUGUGCGAa -3' miRNA: 3'- uCGc---UG-GGGCUGCuGuACGACGCGCU- -5' |
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| 20881 | 3' | -59.1 | NC_004689.1 | + | 60311 | 0.74 | 0.198058 |
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Target: 5'- cGUGACCaCGAUGcggcACAUGUUGCGCGAc -3' miRNA: 3'- uCGCUGGgGCUGC----UGUACGACGCGCU- -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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