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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 | |||||||
| 28339 | 3' | -58 | NC_005946.1 | + | 9325 | 0.66 | 0.717435 |
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Target: 5'- aGGGUGgacGGGAGGACA-GAGGaCagaagGUCc -3' miRNA: 3'- aCCCACa--CCUUCCUGUgCUCC-Gg----CAG- -5' |
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| 28339 | 3' | -58 | NC_005946.1 | + | 14949 | 0.67 | 0.680838 |
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Target: 5'- cGGGcacUGUGccggcggcaaacgcaGAAGGAucgguCACGuAGGCCGUCu -3' miRNA: 3'- aCCC---ACAC---------------CUUCCU-----GUGC-UCCGGCAG- -5' |
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| 28339 | 3' | -58 | NC_005946.1 | + | 83876 | 0.68 | 0.62507 |
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Target: 5'- aGGGUGaGGggGGcCGUGuGGcCCGUCu -3' miRNA: 3'- aCCCACaCCuuCCuGUGCuCC-GGCAG- -5' |
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| 28339 | 3' | -58 | NC_005946.1 | + | 93822 | 0.72 | 0.41912 |
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Target: 5'- gGGGUGUGGGAGGAaagcucCugGAcGCCcUCg -3' miRNA: 3'- aCCCACACCUUCCU------GugCUcCGGcAG- -5' |
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| 28339 | 3' | -58 | NC_005946.1 | + | 85255 | 0.72 | 0.41912 |
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Target: 5'- uUGGGgcuUGGAGGGAgCugGGGGCCa-- -3' miRNA: 3'- -ACCCac-ACCUUCCU-GugCUCCGGcag -5' |
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| 28339 | 3' | -58 | NC_005946.1 | + | 49260 | 0.73 | 0.327967 |
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Target: 5'- cGGGacgaaccUGgagcccaGGAAGGACAgGGGGCUGUCa -3' miRNA: 3'- aCCC-------ACa------CCUUCCUGUgCUCCGGCAG- -5' |
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| 28339 | 3' | -58 | NC_005946.1 | + | 19473 | 0.8 | 0.121273 |
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Target: 5'- -cGGUGUGGAAGGAgGCuauagaGAGGCUGUCg -3' miRNA: 3'- acCCACACCUUCCUgUG------CUCCGGCAG- -5' |
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| 28339 | 3' | -58 | NC_005946.1 | + | 4286 | 1.1 | 0.001049 |
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Target: 5'- gUGGGUGUGGAAGGACACGAGGCCGUCg -3' miRNA: 3'- -ACCCACACCUUCCUGUGCUCCGGCAG- -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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