miRNA: 3'- -CAGUUCCUGUUGaccuaaa---AgUGGUG- -5'
miRNA: 3'- -CAGu---UCCUG-UUGaCCUAaaAGUGGUG- -5'
miRNA: 3'- caGUUCCUGUUGaCCUAAAAgUGG-UG- -5'
miRNA: 3'- -CAGUUCCUGUUGACCUAAAAGUGGUG- -5'
Results 1 - 4 of 4 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 | |||||||
| 27535 | 5' | -46.8 | NC_005879.1 | + | 10707 | 0.66 | 0.970689 |
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Target: 5'- aGUCGGGGACAGCgcuccugcugUgGCCACu -3' miRNA: 3'- -CAGUUCCUGUUGaccuaaa---AgUGGUG- -5' |
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| 27535 | 5' | -46.8 | NC_005879.1 | + | 20104 | 0.66 | 0.968237 |
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Target: 5'- uGUCcgauGGGACuGAC-GGAU--UCACCGCa -3' miRNA: 3'- -CAGu---UCCUG-UUGaCCUAaaAGUGGUG- -5' |
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| 27535 | 5' | -46.8 | NC_005879.1 | + | 33720 | 0.69 | 0.894507 |
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Target: 5'- -gCAAGGGCGAUgGGAUUUUaGCCuACa -3' miRNA: 3'- caGUUCCUGUUGaCCUAAAAgUGG-UG- -5' |
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| 27535 | 5' | -46.8 | NC_005879.1 | + | 33691 | 1.12 | 0.003118 |
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Target: 5'- gGUCAAGGACAACUGGAUUUUCACCACg -3' miRNA: 3'- -CAGUUCCUGUUGACCUAAAAGUGGUG- -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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