miRNA: 3'- aUGCCG-CUAUCGGGCugUCaaGGCcu -5'
miRNA: 3'- aUGCC-GCUAUCGGGC-------UGUCaAG-GC-CU- -5'
miRNA: 3'- aUGCCGCU---AU-CGGGCUGU-CAAG----GCCU- -5'
miRNA: 3'- -AUGCCGCuauCG-GgCugUCAAGGCCU- -5'
miRNA: 3'- -AUGCCGCUAUCGGGCUGUCAAGGCCU- -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 | |||||||
| 27969 | 3' | -56.6 | NC_005886.2 | + | 17712 | 0.66 | 0.581446 |
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Target: 5'- gGCGGCaGGUGGCCCGuuGGccCCGa- -3' miRNA: 3'- aUGCCG-CUAUCGGGCugUCaaGGCcu -5' |
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| 27969 | 3' | -56.6 | NC_005886.2 | + | 19350 | 0.66 | 0.558544 |
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Target: 5'- aACGGaCGAUAGCCCGuuucuucGCAGgUCuCGcGAc -3' miRNA: 3'- aUGCC-GCUAUCGGGC-------UGUCaAG-GC-CU- -5' |
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| 27969 | 3' | -56.6 | NC_005886.2 | + | 29772 | 0.72 | 0.290394 |
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Target: 5'- gACGGCGAaggUAcGCCCGACGuGUUCauugCGGAc -3' miRNA: 3'- aUGCCGCU---AU-CGGGCUGU-CAAG----GCCU- -5' |
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| 27969 | 3' | -56.6 | NC_005886.2 | + | 25653 | 0.72 | 0.28315 |
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Target: 5'- aUGCGGCGc--GCaCgGugAGUUCCGGAa -3' miRNA: 3'- -AUGCCGCuauCG-GgCugUCAAGGCCU- -5' |
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| 27969 | 3' | -56.6 | NC_005886.2 | + | 15272 | 1.07 | 0.000768 |
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Target: 5'- aUACGGCGAUAGCCCGACAGUUCCGGAg -3' miRNA: 3'- -AUGCCGCUAUCGGGCUGUCAAGGCCU- -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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