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miRNA: 3'- -CCGCUGGucUACGCAUAAGCaau--GCU- -5'
miRNA: 3'- -CCGCU-GGUCUa-CGCAU-AAGCa----AUGCU- -5'
miRNA: 3'- -CCGcUGGUCUACGCauAAGCAauGCU- -5'
miRNA: 3'- -CCGCUGGU--------CuaCGCauaAGCAa----UGCU- -5'
Results 1 - 4 of 4 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand | Start Position |
R_P_ratio#
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P value |
| Predicted miRNA align pattern | |||||||
| 12208 | 5' | -48.7 | NC_003309.1 | + | 9558 | 0.72 | 0.7702 |
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Target: 5'- cGGCGGCUu-GUGCGUAUUCGcggauCGAa -3' miRNA: 3'- -CCGCUGGucUACGCAUAAGCaau--GCU- -5' |
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| 12208 | 5' | -48.7 | NC_003309.1 | + | 32862 | 0.71 | 0.839253 |
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Target: 5'- gGGCGAuCCAGAagGCGUGcUUCGcgagcUGCGGg -3' miRNA: 3'- -CCGCU-GGUCUa-CGCAU-AAGCa----AUGCU- -5' |
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| 12208 | 5' | -48.7 | NC_003309.1 | + | 48014 | 0.69 | 0.910888 |
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Target: 5'- aGGUcGCCGGAUGCGauUUCGU--CGAa -3' miRNA: 3'- -CCGcUGGUCUACGCauAAGCAauGCU- -5' |
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| 12208 | 5' | -48.7 | NC_003309.1 | + | 22485 | 0.67 | 0.963085 |
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Target: 5'- cGGCGGCCAccgccgacGcgGCGgcaUCGUgcgcgGCGAu -3' miRNA: 3'- -CCGCUGGU--------CuaCGCauaAGCAa----UGCU- -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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