miRNA: 3'- -GGCAggC-CCGUaAUGCAcGUUGAGCa -5'
miRNA: 3'- -GGCAGG-CCCGUaa------UGC-ACGUUG--AGCA- -5'
miRNA: 3'- -GGCAGGCCCGUaau--GCA-CGUUgaGCA- -5'
miRNA: 3'- -GGCAGG-------CCCGua-----AUGCACGUUGAGca -5'
miRNA: 3'- -GGCAGGCCCGUAAUGCACGUUGAGCA- -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 | |||||||
| 16591 | 3' | -53.3 | NC_004117.1 | + | 48530 | 0.66 | 0.981822 |
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Target: 5'- cUCGUuuGuGGCGcUGCGU-CGGCUCGa -3' miRNA: 3'- -GGCAggC-CCGUaAUGCAcGUUGAGCa -5' |
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| 16591 | 3' | -53.3 | NC_004117.1 | + | 19904 | 0.69 | 0.917173 |
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Target: 5'- aCUGUCCcGGGCAguuucgaaGCGuUGCAACguUCGUg -3' miRNA: 3'- -GGCAGG-CCCGUaa------UGC-ACGUUG--AGCA- -5' |
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| 16591 | 3' | -53.3 | NC_004117.1 | + | 78662 | 0.7 | 0.885352 |
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Target: 5'- gUCGUCCGGGCAggccuCGUgGCAGg-CGUa -3' miRNA: 3'- -GGCAGGCCCGUaau--GCA-CGUUgaGCA- -5' |
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| 16591 | 3' | -53.3 | NC_004117.1 | + | 26439 | 0.7 | 0.855029 |
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Target: 5'- uCCGUCCacguugcGGGCcgccagaUGCGUGUAACUCa- -3' miRNA: 3'- -GGCAGG-------CCCGua-----AUGCACGUUGAGca -5' |
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| 16591 | 3' | -53.3 | NC_004117.1 | + | 112070 | 1.11 | 0.004858 |
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Target: 5'- aCCGUCCGGGCAUUACGUGCAACUCGUa -3' miRNA: 3'- -GGCAGGCCCGUAAUGCACGUUGAGCA- -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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