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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 | |||||||
| 28525 | 3' | -58.6 | NC_005946.1 | + | 26623 | 0.67 | 0.626136 |
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Target: 5'- cAGCUCaggGGGUCCA-GGUaGUCCUuuGCc -3' miRNA: 3'- -UCGAG---CCCAGGUgCCAgUAGGAggUG- -5' |
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| 28525 | 3' | -58.6 | NC_005946.1 | + | 36661 | 0.68 | 0.605535 |
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Target: 5'- gGGCUCGGacucuGUCCACc--CAUCCUCCuCg -3' miRNA: 3'- -UCGAGCC-----CAGGUGccaGUAGGAGGuG- -5' |
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| 28525 | 3' | -58.6 | NC_005946.1 | + | 35825 | 0.68 | 0.585015 |
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Target: 5'- gGGCUgGGGUCCcacuACGGcCAggugccccuUCCUCC-Cg -3' miRNA: 3'- -UCGAgCCCAGG----UGCCaGU---------AGGAGGuG- -5' |
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| 28525 | 3' | -58.6 | NC_005946.1 | + | 55849 | 0.68 | 0.565648 |
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Target: 5'- gAGCUcCGGGUuuugcuccagccUCAUGGUCAgggccuucuuugacgCCUCCGCc -3' miRNA: 3'- -UCGA-GCCCA------------GGUGCCAGUa--------------GGAGGUG- -5' |
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| 28525 | 3' | -58.6 | NC_005946.1 | + | 97224 | 0.69 | 0.541432 |
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Target: 5'- gGGCUCugGGGUCUugGGUUuuugggguuucacuAUCCUCUg- -3' miRNA: 3'- -UCGAG--CCCAGGugCCAG--------------UAGGAGGug -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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