miRNA: 3'- uauaUGCGGC----UCCUCa--CGgAGCCACG- -5'
miRNA: 3'- uauaUGCGg---CUCCUCA----------CGGAGCCACG- -5'
miRNA: 3'- -UAUAUGCGGCUCCUCACGGAGCCACG- -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 | |||||||
| 16662 | 3' | -55.7 | NC_004156.1 | + | 149316 | 0.69 | 0.864904 |
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Target: 5'- ---gGCGUCGguguAGGAGgugGCgUCGGUGUa -3' miRNA: 3'- uauaUGCGGC----UCCUCa--CGgAGCCACG- -5' |
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| 16662 | 3' | -55.7 | NC_004156.1 | + | 163554 | 0.7 | 0.825595 |
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Target: 5'- ---aAUGUaucaGAGGAGUgccgacauggGCCUCGGUGUa -3' miRNA: 3'- uauaUGCGg---CUCCUCA----------CGGAGCCACG- -5' |
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| 16662 | 3' | -55.7 | NC_004156.1 | + | 15788 | 1.1 | 0.003648 |
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Target: 5'- aAUAUACGCCGAGGAGUGCCUCGGUGCa -3' miRNA: 3'- -UAUAUGCGGCUCCUCACGGAGCCACG- -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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