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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 | |||||||
| 28457 | 3' | -56.4 | NC_005946.1 | + | 11146 | 0.66 | 0.823843 |
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Target: 5'- --aGCGCCccuUGGguG--GCGGGUCACa -3' miRNA: 3'- guaUGUGGu--GCCguCagCGCCCAGUG- -5' |
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| 28457 | 3' | -56.4 | NC_005946.1 | + | 26918 | 0.67 | 0.787648 |
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Target: 5'- gCGUACGCCAgGGC---CGgGGGcCACa -3' miRNA: 3'- -GUAUGUGGUgCCGucaGCgCCCaGUG- -5' |
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| 28457 | 3' | -56.4 | NC_005946.1 | + | 28043 | 0.69 | 0.636146 |
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Target: 5'- --gACGUCACGGacuggaAGUCGgGGGUCAUg -3' miRNA: 3'- guaUGUGGUGCCg-----UCAGCgCCCAGUG- -5' |
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| 28457 | 3' | -56.4 | NC_005946.1 | + | 26607 | 0.69 | 0.625675 |
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Target: 5'- --gACGCgGCGGCAGagaaugCGggaGGGUCGCg -3' miRNA: 3'- guaUGUGgUGCCGUCa-----GCg--CCCAGUG- -5' |
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| 28457 | 3' | -56.4 | NC_005946.1 | + | 102942 | 0.7 | 0.594323 |
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Target: 5'- -cUGCACCGCGGaGGUCGCcaGGGccuucUCGCc -3' miRNA: 3'- guAUGUGGUGCCgUCAGCG--CCC-----AGUG- -5' |
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| 28457 | 3' | -56.4 | NC_005946.1 | + | 22415 | 0.71 | 0.512496 |
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Target: 5'- cCAgauCACCACGGCAguggaccacGUCGUGGGUa-- -3' miRNA: 3'- -GUau-GUGGUGCCGU---------CAGCGCCCAgug -5' |
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| 28457 | 3' | -56.4 | NC_005946.1 | + | 69632 | 0.74 | 0.39118 |
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Target: 5'- gGUGgGCUccgGCGGCGGUgGCGGGUCu- -3' miRNA: 3'- gUAUgUGG---UGCCGUCAgCGCCCAGug -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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