miRNA: 3'- -GGACC-GCaCa---GAGGGGAC-GaCGaCGU- -5'
miRNA: 3'- -GGACCGc-ACaGAGGGGACG---ACGACGu -5'
miRNA: 3'- -GGACCGCacagagGGGAC-GACGACGU- -5'
miRNA: 3'- -GGACCgCA---CAGa---GGGGACGACGaCGU- -5'
miRNA: 3'- -GGACCGCACAGAGGGGACGACGACGU- -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 | |||||||
| 28432 | 3' | -59.7 | NC_005946.1 | + | 22170 | 0.66 | 0.658918 |
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Target: 5'- cCCUGGcCGcGgccgCUCCCCUGaCcGCcGCAg -3' miRNA: 3'- -GGACC-GCaCa---GAGGGGAC-GaCGaCGU- -5' |
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| 28432 | 3' | -59.7 | NC_005946.1 | + | 90628 | 0.67 | 0.586923 |
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Target: 5'- uCUUGGUcaUGcCUCCCCUGCcuaUGUUGCu -3' miRNA: 3'- -GGACCGc-ACaGAGGGGACG---ACGACGu -5' |
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| 28432 | 3' | -59.7 | NC_005946.1 | + | 44699 | 0.68 | 0.546343 |
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Target: 5'- cCCUGGUGg-----CCCUGaCUGCUGCAc -3' miRNA: 3'- -GGACCGCacagagGGGAC-GACGACGU- -5' |
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| 28432 | 3' | -59.7 | NC_005946.1 | + | 87238 | 0.69 | 0.477789 |
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Target: 5'- gCCUGG-GUuccGUCagagCCCUUGCUGCgGCAa -3' miRNA: 3'- -GGACCgCA---CAGa---GGGGACGACGaCGU- -5' |
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| 28432 | 3' | -59.7 | NC_005946.1 | + | 83424 | 1.1 | 0.000699 |
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Target: 5'- cCCUGGCGUGUCUCCCCUGCUGCUGCAu -3' miRNA: 3'- -GGACCGCACAGAGGGGACGACGACGU- -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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