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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand | Start Position |
R_P_ratio #
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P value |
| Predicted miRNA align pattern | |||||||
| 28454 | 5' | -55.6 | NC_005946.1 | + | 16168 | 0.66 | 0.851845 |
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Target: 5'- cGGGCAGccaccCGGCGGCC-CUu--UCCa -3' miRNA: 3'- -CCUGUCca---GCCGCCGGaGAuauAGGc -5' |
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| 28454 | 5' | -55.6 | NC_005946.1 | + | 49605 | 0.66 | 0.882158 |
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Target: 5'- aGACaAGGUgGGagacguCGGCCUCUGccgCCGg -3' miRNA: 3'- cCUG-UCCAgCC------GCCGGAGAUauaGGC- -5' |
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| 28454 | 5' | -55.6 | NC_005946.1 | + | 14283 | 0.66 | 0.889175 |
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Target: 5'- aGGCAGGcCGGCguacaGGCaCUCUGcGUCgGa -3' miRNA: 3'- cCUGUCCaGCCG-----CCG-GAGAUaUAGgC- -5' |
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| 28454 | 5' | -55.6 | NC_005946.1 | + | 31391 | 0.66 | 0.889175 |
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Target: 5'- uGAC-GG-CGGCGGCCUCc---UCCu -3' miRNA: 3'- cCUGuCCaGCCGCCGGAGauauAGGc -5' |
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| 28454 | 5' | -55.6 | NC_005946.1 | + | 30198 | 0.69 | 0.703002 |
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Target: 5'- uGGACuccAGGaugUCGGCGGCCUCUcccuUGUUg- -3' miRNA: 3'- -CCUG---UCC---AGCCGCCGGAGAu---AUAGgc -5' |
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| 28454 | 5' | -55.6 | NC_005946.1 | + | 26656 | 0.69 | 0.743229 |
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Target: 5'- uGGAgAGGacccucgCGGCGGCCUCUgcgacuAUGgacgCCa -3' miRNA: 3'- -CCUgUCCa------GCCGCCGGAGA------UAUa---GGc -5' |
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| 28454 | 5' | -55.6 | NC_005946.1 | + | 85116 | 0.7 | 0.640989 |
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Target: 5'- cGACAGGcuccUGGagcaGGCCUCggccGUGUCCGg -3' miRNA: 3'- cCUGUCCa---GCCg---CCGGAGa---UAUAGGC- -5' |
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| 28454 | 5' | -55.6 | NC_005946.1 | + | 65615 | 0.7 | 0.65763 |
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Target: 5'- uGGACGGGcUCGGaCGGCCUgacggccucUCCGg -3' miRNA: 3'- -CCUGUCC-AGCC-GCCGGAgauau----AGGC- -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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