miRNA: 3'- uuaagUCGCAUGGUCGCGcUAAg-----GCC- -5'
miRNA: 3'- uuaaGUCGCA----UGGUCGCGCU-------AAGGcc -5'
miRNA: 3'- -UUAAGUCGCA--------UGGUCGCGCUaaGGCC- -5'
miRNA: 3'- uuAAGUCGCa-UGGUCGCGCuaaGGCC- -5'
miRNA: 3'- -UUAAGUCGCAUGGUCGCGCUAAGGCC- -5'
Results 1 - 5 of 5 are showing below:
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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 | |||||||
| 27361 | 5' | -52.3 | NC_005857.1 | + | 16807 | 0.66 | 0.836874 |
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Target: 5'- ----gGGCGUAUCAGCGCaGUUaauggaCGGg -3' miRNA: 3'- uuaagUCGCAUGGUCGCGcUAAg-----GCC- -5' |
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| 27361 | 5' | -52.3 | NC_005857.1 | + | 37584 | 0.7 | 0.634711 |
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Target: 5'- ---gCAGCGUaucgACCAGCGCGGcgggaaaUUCCa- -3' miRNA: 3'- uuaaGUCGCA----UGGUCGCGCU-------AAGGcc -5' |
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| 27361 | 5' | -52.3 | NC_005857.1 | + | 42788 | 0.78 | 0.229444 |
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Target: 5'- cGGUUCGGCGUcuauugcgGCCAGCGCGAacUCGGc -3' miRNA: 3'- -UUAAGUCGCA--------UGGUCGCGCUaaGGCC- -5' |
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| 27361 | 5' | -52.3 | NC_005857.1 | + | 8097 | 0.82 | 0.127624 |
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Target: 5'- -cUUCAGCGccGCCAGCGCGucgCCGGg -3' miRNA: 3'- uuAAGUCGCa-UGGUCGCGCuaaGGCC- -5' |
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| 27361 | 5' | -52.3 | NC_005857.1 | + | 5725 | 1.08 | 0.002203 |
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Target: 5'- cAAUUCAGCGUACCAGCGCGAUUCCGGc -3' miRNA: 3'- -UUAAGUCGCAUGGUCGCGCUAAGGCC- -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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