miRNA: 3'- -CGcCGGGCa-CGaGGGGAGUCGg---GGGC- -5'
miRNA: 3'- cgCCGGGCACGa-----GGGGAGUCGG-GGGc -5'
miRNA: 3'- -CGCCGGg-----CACGAG-------GGGAGUCGGGggC- -5'
miRNA: 3'- -CGCCGGGCACGAGGGGAGUCGGGGGC- -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 | |||||||
| 31696 | 3' | -66 | NC_006934.1 | + | 1951 | 0.67 | 0.034648 |
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Target: 5'- cGCuGCCCGgaGC-CCCCUCAGCaagaUCUGg -3' miRNA: 3'- -CGcCGGGCa-CGaGGGGAGUCGg---GGGC- -5' |
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| 31696 | 3' | -66 | NC_006934.1 | + | 3960 | 0.68 | 0.027769 |
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Target: 5'- -gGGCCUGUGUgagcacUCCCUUGGCCgCCCc -3' miRNA: 3'- cgCCGGGCACGa-----GGGGAGUCGG-GGGc -5' |
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| 31696 | 3' | -66 | NC_006934.1 | + | 3925 | 0.69 | 0.023624 |
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Target: 5'- gGCGGCCaagggaGUGCUCacacaggCCCUCGGUCCauGg -3' miRNA: 3'- -CGCCGGg-----CACGAG-------GGGAGUCGGGggC- -5' |
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| 31696 | 3' | -66 | NC_006934.1 | + | 1307 | 1.09 | 0.000005 |
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Target: 5'- gGCGGCCCGUGCUCCCCUCAGCCCCCGa -3' miRNA: 3'- -CGCCGGGCACGAGGGGAGUCGGGGGC- -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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