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| ID | Location | Perfect MFE.* | RefSeq Acc. |
strand
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Start Position | R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 21263 | 3' | -52.9 | NC_004778.3 | + | 85482 | 0.66 | 0.957597 |
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Target: 5'- uGUC---AUGGACGCGGgcguuuGCGGCGgCGa -3' miRNA: 3'- gCAGcaaUACCUGCGUU------UGCCGCgGU- -5' |
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| 21263 | 3' | -52.9 | NC_004778.3 | + | 121701 | 0.66 | 0.957597 |
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Target: 5'- gGcCGgcGUGGGCGUGuugcuggccGGCGGCGCUu -3' miRNA: 3'- gCaGCaaUACCUGCGU---------UUGCCGCGGu -5' |
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| 21263 | 3' | -52.9 | NC_004778.3 | + | 98923 | 0.67 | 0.953649 |
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Target: 5'- gCGUCGcuggggAUGGugGCGGcuugcACGcGCGCUg -3' miRNA: 3'- -GCAGCaa----UACCugCGUU-----UGC-CGCGGu -5' |
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| 21263 | 3' | -52.9 | NC_004778.3 | + | 65460 | 0.67 | 0.945028 |
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Target: 5'- gGUCGUugcccgauucUGUGcaaacguuGGCGCGGugGGCGuCCAu -3' miRNA: 3'- gCAGCA----------AUAC--------CUGCGUUugCCGC-GGU- -5' |
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| 21263 | 3' | -52.9 | NC_004778.3 | + | 85516 | 0.67 | 0.945028 |
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Target: 5'- gCGaUGUcAUGGACGCGGgcguuuGCGGCGgCGa -3' miRNA: 3'- -GCaGCAaUACCUGCGUU------UGCCGCgGU- -5' |
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| 21263 | 3' | -52.9 | NC_004778.3 | + | 20478 | 0.68 | 0.930237 |
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Target: 5'- cCGUgCGUUGUGc-CGCcGAUGGUGCCGu -3' miRNA: 3'- -GCA-GCAAUACcuGCGuUUGCCGCGGU- -5' |
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| 21263 | 3' | -52.9 | NC_004778.3 | + | 21655 | 0.68 | 0.924804 |
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Target: 5'- -uUCGgcc--GGCGguGGCGGCGCCAu -3' miRNA: 3'- gcAGCaauacCUGCguUUGCCGCGGU- -5' |
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| 21263 | 3' | -52.9 | NC_004778.3 | + | 38263 | 0.68 | 0.919119 |
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Target: 5'- --------cGGACGCGGACGGCGUg- -3' miRNA: 3'- gcagcaauaCCUGCGUUUGCCGCGgu -5' |
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| 21263 | 3' | -52.9 | NC_004778.3 | + | 22449 | 0.68 | 0.919119 |
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Target: 5'- uGUCGU--UGGugGCGGGC-GCGCa- -3' miRNA: 3'- gCAGCAauACCugCGUUUGcCGCGgu -5' |
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| 21263 | 3' | -52.9 | NC_004778.3 | + | 85570 | 0.66 | 0.971078 |
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Target: 5'- aCGUCauacgcGUGGGCGaCGuguACGGCGUCGc -3' miRNA: 3'- -GCAGcaa---UACCUGC-GUu--UGCCGCGGU- -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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