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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 | |||||||
| 28464 | 3' | -55.2 | NC_005946.1 | + | 10851 | 0.66 | 0.876404 |
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Target: 5'- -cCACCAuCCUGA---GGGcCAUGCCc -3' miRNA: 3'- gaGUGGUcGGACUcuaCCCaGUACGG- -5' |
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| 28464 | 3' | -55.2 | NC_005946.1 | + | 85308 | 0.66 | 0.868853 |
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Target: 5'- uCUCAagAGCCUGAccGAgcagacUGuGGUCGUGUCg -3' miRNA: 3'- -GAGUggUCGGACU--CU------AC-CCAGUACGG- -5' |
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| 28464 | 3' | -55.2 | NC_005946.1 | + | 21009 | 0.66 | 0.860286 |
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Target: 5'- cCUCGCaauCAGaCCUgcGAGGUGGGUCAaggacaggguguuUGCg -3' miRNA: 3'- -GAGUG---GUC-GGA--CUCUACCCAGU-------------ACGg -5' |
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| 28464 | 3' | -55.2 | NC_005946.1 | + | 59598 | 0.66 | 0.853077 |
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Target: 5'- --gACUucuCCUGAGggGGGUCcacAUGCCg -3' miRNA: 3'- gagUGGuc-GGACUCuaCCCAG---UACGG- -5' |
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| 28464 | 3' | -55.2 | NC_005946.1 | + | 59487 | 0.66 | 0.844863 |
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Target: 5'- -aUAUCAGCgUGAGGUGGuGUCAcgGUa -3' miRNA: 3'- gaGUGGUCGgACUCUACC-CAGUa-CGg -5' |
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| 28464 | 3' | -55.2 | NC_005946.1 | + | 36039 | 0.67 | 0.836444 |
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Target: 5'- aUCACCAGCUUGuAGAggacGGcCAUGUa -3' miRNA: 3'- gAGUGGUCGGAC-UCUac--CCaGUACGg -5' |
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| 28464 | 3' | -55.2 | NC_005946.1 | + | 48642 | 0.67 | 0.810026 |
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Target: 5'- aUCGCUAGCCUGAuuacgGGGa-GUGCUa -3' miRNA: 3'- gAGUGGUCGGACUcua--CCCagUACGG- -5' |
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| 28464 | 3' | -55.2 | NC_005946.1 | + | 71047 | 0.71 | 0.617658 |
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Target: 5'- cCUgGCCAGCCUGAaGgcGGGagCGUGaCCc -3' miRNA: 3'- -GAgUGGUCGGACU-CuaCCCa-GUAC-GG- -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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