miRNA: 3'- accaCGAc--UUGGaCGACCGUCUCCGc -5'
miRNA: 3'- -ACCaCGacUUGGACGa---------CCGUCUCCGc -5'
miRNA: 3'- -ACC-ACGACU-----UGG----ACG--ACCGuCUCCGC- -5'
miRNA: 3'- -ACC-ACGAC------UUGGACGACCG--UCUCCGC- -5'
miRNA: 3'- -ACCACGACUUGGACGACCGUCUCCGC- -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 | |||||||
| 17477 | 5' | -58.2 | NC_004456.1 | + | 12126 | 0.67 | 0.414813 |
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Target: 5'- ---aGCUuuuAGCCgGUUGGCAGAGGCu -3' miRNA: 3'- accaCGAc--UUGGaCGACCGUCUCCGc -5' |
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| 17477 | 5' | -58.2 | NC_004456.1 | + | 12483 | 0.67 | 0.405373 |
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Target: 5'- gUGG-GC--GACCUGCcccagcuuggGGCAGGGGCa -3' miRNA: 3'- -ACCaCGacUUGGACGa---------CCGUCUCCGc -5' |
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| 17477 | 5' | -58.2 | NC_004456.1 | + | 8842 | 0.68 | 0.318775 |
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Target: 5'- gUGGcUGCUGAuaaccGCCuuguUGCugUGGCuGAGGCGc -3' miRNA: 3'- -ACC-ACGACU-----UGG----ACG--ACCGuCUCCGC- -5' |
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| 17477 | 5' | -58.2 | NC_004456.1 | + | 22344 | 0.78 | 0.074076 |
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Target: 5'- uUGGaUGCUGcggcccAGCCUGCUGGCuaAGGGGUGa -3' miRNA: 3'- -ACC-ACGAC------UUGGACGACCG--UCUCCGC- -5' |
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| 17477 | 5' | -58.2 | NC_004456.1 | + | 19347 | 1.09 | 0.0003 |
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Target: 5'- gUGGUGCUGAACCUGCUGGCAGAGGCGa -3' miRNA: 3'- -ACCACGACUUGGACGACCGUCUCCGC- -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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