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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 | |||||||
| 18028 | 5' | -58 | NC_004665.1 | + | 29079 | 0.66 | 0.460093 |
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Target: 5'- --cACGcUCGCCGGGGuuGuCCGCa--- -3' miRNA: 3'- auuUGC-AGUGGCCCCggC-GGUGguac -5' |
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| 18028 | 5' | -58 | NC_004665.1 | + | 24516 | 0.66 | 0.454036 |
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Target: 5'- -cAAC-UCACuCGGGGCUGUcuucgcuaaggagcaCACCAUGa -3' miRNA: 3'- auUUGcAGUG-GCCCCGGCG---------------GUGGUAC- -5' |
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| 18028 | 5' | -58 | NC_004665.1 | + | 37225 | 0.67 | 0.401574 |
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Target: 5'- cAGAgGUCACCGGGGagagGCUcCUAUGg -3' miRNA: 3'- aUUUgCAGUGGCCCCgg--CGGuGGUAC- -5' |
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| 18028 | 5' | -58 | NC_004665.1 | + | 119 | 0.67 | 0.401574 |
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Target: 5'- cAGAgGUCACCGGGGagagGCUcCUAUGg -3' miRNA: 3'- aUUUgCAGUGGCCCCgg--CGGuGGUAC- -5' |
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| 18028 | 5' | -58 | NC_004665.1 | + | 3113 | 0.7 | 0.256826 |
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Target: 5'- gUGAGCGUCGuuGuGGUCGCUGCUGUGg -3' miRNA: 3'- -AUUUGCAGUggCcCCGGCGGUGGUAC- -5' |
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| 18028 | 5' | -58 | NC_004665.1 | + | 15697 | 0.7 | 0.24368 |
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Target: 5'- ------aCACCGGGGauGCCACCAUa -3' miRNA: 3'- auuugcaGUGGCCCCggCGGUGGUAc -5' |
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| 18028 | 5' | -58 | NC_004665.1 | + | 32758 | 1.05 | 0.000544 |
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Target: 5'- cUAAACGUCACCGGGGCCGCCACCAUGc -3' miRNA: 3'- -AUUUGCAGUGGCCCCGGCGGUGGUAC- -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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