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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 | |||||||
| 28355 | 5' | -51.6 | NC_005946.1 | + | 19681 | 0.66 | 0.94746 |
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Target: 5'- uGCGCAAGGGAggccgagaggGCCUCgGgUCAGu-- -3' miRNA: 3'- -UGCGUUUCUUa---------CGGAGgCgAGUCuaa -5' |
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| 28355 | 5' | -51.6 | NC_005946.1 | + | 80386 | 0.67 | 0.912711 |
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Target: 5'- cCGCAAAGAGgaccagccugucccUGCCUUCGgaCAGGg- -3' miRNA: 3'- uGCGUUUCUU--------------ACGGAGGCgaGUCUaa -5' |
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| 28355 | 5' | -51.6 | NC_005946.1 | + | 76731 | 0.69 | 0.855618 |
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Target: 5'- gGCGCAAAGGG-GCC-CCGCgggcgCAGGc- -3' miRNA: 3'- -UGCGUUUCUUaCGGaGGCGa----GUCUaa -5' |
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| 28355 | 5' | -51.6 | NC_005946.1 | + | 60952 | 0.69 | 0.829433 |
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Target: 5'- -gGCGGAGGAUGCCucUCCGUcucugUCAGGg- -3' miRNA: 3'- ugCGUUUCUUACGG--AGGCG-----AGUCUaa -5' |
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| 28355 | 5' | -51.6 | NC_005946.1 | + | 36982 | 0.7 | 0.788695 |
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Target: 5'- aGCGUGuaucAGGAUGCCUCCGCcccucuccuccaccUCGGAg- -3' miRNA: 3'- -UGCGUu---UCUUACGGAGGCG--------------AGUCUaa -5' |
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| 28355 | 5' | -51.6 | NC_005946.1 | + | 15982 | 1.06 | 0.006243 |
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Target: 5'- aACGCAAAGAAUGCCUCCGCUCAGAUUa -3' miRNA: 3'- -UGCGUUUCUUACGGAGGCGAGUCUAA- -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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