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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 | |||||||
| 28367 | 3' | -57.9 | NC_005946.1 | + | 19579 | 0.66 | 0.787996 |
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Target: 5'- uCUGUCCUugccucugcCGACGGGaGGCaaGAgugcUGCUGg -3' miRNA: 3'- -GGCAGGA---------GCUGCCC-CUGgaCU----ACGAC- -5' |
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| 28367 | 3' | -57.9 | NC_005946.1 | + | 42158 | 0.66 | 0.760003 |
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Target: 5'- aCGUCC-CcACGGGGACCgucUGCg- -3' miRNA: 3'- gGCAGGaGcUGCCCCUGGacuACGac -5' |
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| 28367 | 3' | -57.9 | NC_005946.1 | + | 72713 | 0.66 | 0.759051 |
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Target: 5'- gCGUCCguggacgUgGACGGGGuCCUG-UGCg- -3' miRNA: 3'- gGCAGG-------AgCUGCCCCuGGACuACGac -5' |
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| 28367 | 3' | -57.9 | NC_005946.1 | + | 89864 | 0.67 | 0.750434 |
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Target: 5'- cCCGguggCCUCGcCGGGGACgaUGAccgUGCc- -3' miRNA: 3'- -GGCa---GGAGCuGCCCCUGg-ACU---ACGac -5' |
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| 28367 | 3' | -57.9 | NC_005946.1 | + | 47485 | 0.69 | 0.599503 |
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Target: 5'- aUGUCCUUGA-GGGG-CUUGGUGuCUGg -3' miRNA: 3'- gGCAGGAGCUgCCCCuGGACUAC-GAC- -5' |
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| 28367 | 3' | -57.9 | NC_005946.1 | + | 2297 | 0.69 | 0.578189 |
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Target: 5'- gUGUCCUCGGacgcggaccccgcCGGGGG-CUGGUGCa- -3' miRNA: 3'- gGCAGGAGCU-------------GCCCCUgGACUACGac -5' |
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| 28367 | 3' | -57.9 | NC_005946.1 | + | 69611 | 0.72 | 0.462179 |
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Target: 5'- cCUGUCCUCca-GGaGGGCCUGA-GCUGu -3' miRNA: 3'- -GGCAGGAGcugCC-CCUGGACUaCGAC- -5' |
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| 28367 | 3' | -57.9 | NC_005946.1 | + | 25884 | 1.11 | 0.001164 |
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Target: 5'- cCCGUCCUCGACGGGGACCUGAUGCUGg -3' miRNA: 3'- -GGCAGGAGCUGCCCCUGGACUACGAC- -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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