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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 | |||||||
| 31998 | 3' | -48.5 | NC_006949.1 | + | 46632 | 0.66 | 0.93656 |
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Target: 5'- -cGCAGCCcuuaAUGGGagcuccUUCUGCGUGAGUg -3' miRNA: 3'- guCGUUGG----UAUCU------GAGACGUAUUCGu -5' |
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| 31998 | 3' | -48.5 | NC_006949.1 | + | 36910 | 0.66 | 0.930722 |
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Target: 5'- gCAGUAGCUA-AGGCUUUGgCAUuAGCGa -3' miRNA: 3'- -GUCGUUGGUaUCUGAGAC-GUAuUCGU- -5' |
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| 31998 | 3' | -48.5 | NC_006949.1 | + | 40552 | 0.7 | 0.774365 |
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Target: 5'- aCAGCAaugaACCGUGGAUUCaaaaGCAUuucuGGCAu -3' miRNA: 3'- -GUCGU----UGGUAUCUGAGa---CGUAu---UCGU- -5' |
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| 31998 | 3' | -48.5 | NC_006949.1 | + | 43028 | 0.71 | 0.718016 |
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Target: 5'- cCAGaagGCgAUGGAUuaUCUGCAUGAGCGa -3' miRNA: 3'- -GUCgu-UGgUAUCUG--AGACGUAUUCGU- -5' |
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| 31998 | 3' | -48.5 | NC_006949.1 | + | 9423 | 0.72 | 0.68289 |
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Target: 5'- cCAGCGcuuACCAgcGACUCgGCAUGAuGCGc -3' miRNA: 3'- -GUCGU---UGGUauCUGAGaCGUAUU-CGU- -5' |
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| 31998 | 3' | -48.5 | NC_006949.1 | + | 16367 | 1.1 | 0.002932 |
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Target: 5'- gCAGCAACCAUAGACUCUGCAUAAGCAg -3' miRNA: 3'- -GUCGUUGGUAUCUGAGACGUAUUCGU- -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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