miRNA: 3'- acGGCA-UCGGUCUGG------CGC-AGGA-CCCC- -5'
miRNA: 3'- aCGGCa---UCGGucu-GGCGCAGGaCCCC- -5'
miRNA: 3'- aCGgCAUCGGUCUGGCgCAggACCCC- -5'
miRNA: 3'- -ACGGCauCGGU-CUGGCGCa-GGAC-CCC- -5'
miRNA: 3'- -ACGGCAUCGGUCUGGCGCAGGACCCC- -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 | |||||||
| 688 | 3' | -60.7 | AC_000018.1 | + | 27773 | 0.67 | 0.298678 |
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Target: 5'- -uCCGUgGGCCGGACCcugaggGUGcUCCUcGGGGa -3' miRNA: 3'- acGGCA-UCGGUCUGG------CGC-AGGA-CCCC- -5' |
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| 688 | 3' | -60.7 | AC_000018.1 | + | 23677 | 0.68 | 0.250443 |
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Target: 5'- gGCUGgcagAGCCcauuCCGCGUUCgGGGGu -3' miRNA: 3'- aCGGCa---UCGGucu-GGCGCAGGaCCCC- -5' |
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| 688 | 3' | -60.7 | AC_000018.1 | + | 23930 | 0.68 | 0.244101 |
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Target: 5'- gGUgGUAGCUGGACUGgGUggUGGGGu -3' miRNA: 3'- aCGgCAUCGGUCUGGCgCAggACCCC- -5' |
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| 688 | 3' | -60.7 | AC_000018.1 | + | 16287 | 0.72 | 0.124816 |
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Target: 5'- cUGCUGccGCCGuGGCCGCGcgCCUGcGGGa -3' miRNA: 3'- -ACGGCauCGGU-CUGGCGCa-GGAC-CCC- -5' |
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| 688 | 3' | -60.7 | AC_000018.1 | + | 18417 | 1.1 | 0.000137 |
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Target: 5'- uUGCCGUAGCCAGACCGCGUCCUGGGGg -3' miRNA: 3'- -ACGGCAUCGGUCUGGCGCAGGACCCC- -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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