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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 | |||||||
| 13054 | 3' | -55 | NC_003390.1 | + | 5265 | 0.66 | 0.634887 |
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Target: 5'- -cUGGAUCACACCCaccagCUgGGCaucacUCAGGa -3' miRNA: 3'- uuACCUGGUGUGGGa----GA-CCGa----AGUCU- -5' |
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| 13054 | 3' | -55 | NC_003390.1 | + | 24235 | 0.67 | 0.578344 |
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Target: 5'- cAAUGGugACCAgGCCCUCagGGCggCGGc -3' miRNA: 3'- -UUACC--UGGUgUGGGAGa-CCGaaGUCu -5' |
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| 13054 | 3' | -55 | NC_003390.1 | + | 13801 | 0.68 | 0.544905 |
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Target: 5'- --gGGACCGCAguCCCUCUuGGUga-AGAg -3' miRNA: 3'- uuaCCUGGUGU--GGGAGA-CCGaagUCU- -5' |
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| 13054 | 3' | -55 | NC_003390.1 | + | 28000 | 0.68 | 0.533893 |
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Target: 5'- uGAUGGAauUCAuCACCaCUCUGGCg-CAGAc -3' miRNA: 3'- -UUACCU--GGU-GUGG-GAGACCGaaGUCU- -5' |
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| 13054 | 3' | -55 | NC_003390.1 | + | 9475 | 0.68 | 0.501365 |
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Target: 5'- --aGGGCCAUACUgUUUGGCcacuuugUCGGAg -3' miRNA: 3'- uuaCCUGGUGUGGgAGACCGa------AGUCU- -5' |
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| 13054 | 3' | -55 | NC_003390.1 | + | 32222 | 0.68 | 0.490715 |
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Target: 5'- aGGUGGGCCACugCUUC-GGCUUg--- -3' miRNA: 3'- -UUACCUGGUGugGGAGaCCGAAgucu -5' |
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| 13054 | 3' | -55 | NC_003390.1 | + | 10077 | 0.76 | 0.15945 |
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Target: 5'- -uUGGcgGCCAgGCCCUCUGGgaUCAGGc -3' miRNA: 3'- uuACC--UGGUgUGGGAGACCgaAGUCU- -5' |
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| 13054 | 3' | -55 | NC_003390.1 | + | 3897 | 1.07 | 0.000976 |
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Target: 5'- gAAUGGACCACACCCUCUGGCUUCAGAg -3' miRNA: 3'- -UUACCUGGUGUGGGAGACCGAAGUCU- -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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