miRNA: 3'- acGAUGAGUAGU-------------AGGGuGUGGU-AGUG- -5'
miRNA: 3'- -ACGAUGagUAGUa--------GGGUGUGGUAGUG- -5'
miRNA: 3'- aCGaugaGUAGUA---GGGUGUGGUAGUG- -5'
miRNA: 3'- -ACGAUGAGUAGua-G-GGUGUGGUaGUg -5'
miRNA: 3'- -ACGAUGAGUAGUAGGGUGUGGUAGUG- -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 | |||||||
| 20964 | 3' | -51.1 | NC_004724.1 | + | 1572 | 0.66 | 0.564407 |
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Target: 5'- -cCUGCUCAUCAggacagcgggaacUUCC-CGCCAcUCACg -3' miRNA: 3'- acGAUGAGUAGU-------------AGGGuGUGGU-AGUG- -5' |
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| 20964 | 3' | -51.1 | NC_004724.1 | + | 11687 | 0.67 | 0.504962 |
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Target: 5'- cUGUUAUuaGUCGauugcgcggCUCACACCAUCGCa -3' miRNA: 3'- -ACGAUGagUAGUa--------GGGUGUGGUAGUG- -5' |
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| 20964 | 3' | -51.1 | NC_004724.1 | + | 3247 | 0.68 | 0.458513 |
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Target: 5'- aGCgaugCAUCGUaaaCCUGCACCAUCAUc -3' miRNA: 3'- aCGaugaGUAGUA---GGGUGUGGUAGUG- -5' |
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| 20964 | 3' | -51.1 | NC_004724.1 | + | 2249 | 0.69 | 0.373073 |
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Target: 5'- cUGCUGCUCGUCuuaCgCCGCACUAgCAa -3' miRNA: 3'- -ACGAUGAGUAGua-G-GGUGUGGUaGUg -5' |
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| 20964 | 3' | -51.1 | NC_004724.1 | + | 10289 | 1.1 | 0.000361 |
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Target: 5'- gUGCUACUCAUCAUCCCACACCAUCACu -3' miRNA: 3'- -ACGAUGAGUAGUAGGGUGUGGUAGUG- -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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