miRNA: 3'- -ACCUCUGUcACAGAGG---------UCUC--------------CCCGCa -5'
miRNA: 3'- -ACCUCUGUCACa-------GAGgucUCCCCGCa -5'
miRNA: 3'- -ACCUCUGUCACAGAGGUCUCCCCGCA- -5'
Results 1 - 3 of 3 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 | |||||||
| 2259 | 5' | -58.2 | NC_001405.1 | + | 18393 | 0.69 | 0.287394 |
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Target: 5'- cUGGAGACAcUGUCUCCacggccgguGGAGgcuccucuacgggaGGGCGg -3' miRNA: 3'- -ACCUCUGUcACAGAGG---------UCUC--------------CCCGCa -5' |
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| 2259 | 5' | -58.2 | NC_001405.1 | + | 24183 | 0.7 | 0.235107 |
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Target: 5'- gUGGAGGCGGUGguggcgaaCUCaaaGGGGGCGg -3' miRNA: 3'- -ACCUCUGUCACa-------GAGgucUCCCCGCa -5' |
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| 2259 | 5' | -58.2 | NC_001405.1 | + | 18340 | 1.08 | 0.000341 |
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Target: 5'- gUGGAGACAGUGUCUCCAGAGGGGCGUg -3' miRNA: 3'- -ACCUCUGUCACAGAGGUCUCCCCGCA- -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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