miRNA: 3'- aCGa---UGAGU-----UCCCCa-GGCCCa-GGUCC- -5'
miRNA: 3'- aCGA----UGAGUu---CCCCA--GGC-CCAGGUC-C- -5'
miRNA: 3'- -ACGAUGAGuu--CCCC--AGG-CCCa----GGUCC- -5'
miRNA: 3'- aCgaUGa--GUUCCCCa-GGCCCAGGUCC- -5'
miRNA: 3'- -ACGAUGAGUUCCCCAGGCCCAGGUCC- -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 | |||||||
| 11908 | 3' | -57.8 | NC_003266.2 | + | 10102 | 0.66 | 0.47534 |
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Target: 5'- gGCcaucGCUCGguggcGGGGGcgCCGGGcgCUAGGu -3' miRNA: 3'- aCGa---UGAGU-----UCCCCa-GGCCCa-GGUCC- -5' |
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| 11908 | 3' | -57.8 | NC_003266.2 | + | 16513 | 0.68 | 0.344553 |
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Target: 5'- gGCUuaagACUCGgcguGGGGUugCCGuGGUCCAGcGg -3' miRNA: 3'- aCGA----UGAGUu---CCCCA--GGC-CCAGGUC-C- -5' |
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| 11908 | 3' | -57.8 | NC_003266.2 | + | 25468 | 0.68 | 0.336256 |
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Target: 5'- uUGCUGCUUccucGGGGcaUCCuGGGggaagCCGGGg -3' miRNA: 3'- -ACGAUGAGuu--CCCC--AGG-CCCa----GGUCC- -5' |
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| 11908 | 3' | -57.8 | NC_003266.2 | + | 17776 | 0.75 | 0.111905 |
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Target: 5'- cGgaGCcggCGGGGGGaaCCGGGUCCAGGc -3' miRNA: 3'- aCgaUGa--GUUCCCCa-GGCCCAGGUCC- -5' |
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| 11908 | 3' | -57.8 | NC_003266.2 | + | 33340 | 1.11 | 0.000249 |
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Target: 5'- cUGCUACUCAAGGGGUCCGGGUCCAGGg -3' miRNA: 3'- -ACGAUGAGUUCCCCAGGCCCAGGUCC- -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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