miRNA: 3'- -GGCCGGA-GGGUUCaCAGg---GgUGCAGu -5'
miRNA: 3'- gGCCGG----------AGGGUUCacaGGGGUG-CAGU- -5'
miRNA: 3'- gGCCGGag--------GGU-UCACAGg---GGUGCAGu -5'
miRNA: 3'- -GGCCGG---AGG-GUUCacaGGGGuGCAGU- -5'
Results 21 - 24 of 24 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 | |||||||
| 15684 | 3' | -59 | NC_004065.1 | + | 120874 | 0.66 | 0.900038 |
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Target: 5'- aCCGGCUUgCCCGGG-GUCagggCgGCGUCu -3' miRNA: 3'- -GGCCGGA-GGGUUCaCAGg---GgUGCAGu -5' |
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| 15684 | 3' | -59 | NC_004065.1 | + | 50343 | 0.66 | 0.900038 |
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Target: 5'- gUGGCCaccgccgcgaUCCCGAGcccCCCCGCuGUCAu -3' miRNA: 3'- gGCCGG----------AGGGUUCacaGGGGUG-CAGU- -5' |
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| 15684 | 3' | -59 | NC_004065.1 | + | 29333 | 0.66 | 0.900038 |
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Target: 5'- aCGGCCgcgaaguagaCCAuGGUGUCagaaCCGCGUCc -3' miRNA: 3'- gGCCGGag--------GGU-UCACAGg---GGUGCAGu -5' |
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| 15684 | 3' | -59 | NC_004065.1 | + | 33241 | 0.66 | 0.900038 |
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Target: 5'- aCCGGCCuggUCCgCGAGg--CCUC-CGUCAu -3' miRNA: 3'- -GGCCGG---AGG-GUUCacaGGGGuGCAGU- -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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