miRNA: 3'- -UUGGGAU--UG--UGUGU-CCUAGg--UGGCGG- -5'
miRNA: 3'- -UUGGGAUUGuGu----GUCCU-----AGGUGGcGG- -5'
miRNA: 3'- uuGGGauu----GUGU-----GUCCUAGGUGGCGg -5'
miRNA: 3'- -UUGGGAUUGUGUGUCCUAGGUGGCGG- -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# |
P value
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| Predicted miRNA align pattern | |||||||
| 6160 | 3' | -54.3 | NC_001837.1 | + | 8722 | 0.66 | 0.260406 |
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Target: 5'- cAGCCUUAagGCggGCACAgGGAUCaguGCCGUCg -3' miRNA: 3'- -UUGGGAU--UG--UGUGU-CCUAGg--UGGCGG- -5' |
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| 6160 | 3' | -54.3 | NC_001837.1 | + | 7982 | 0.67 | 0.224059 |
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Target: 5'- uGGCCCUGGC-CuucuuCAGGGccucgUCCACCaCCg -3' miRNA: 3'- -UUGGGAUUGuGu----GUCCU-----AGGUGGcGG- -5' |
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| 6160 | 3' | -54.3 | NC_001837.1 | + | 6335 | 0.68 | 0.169501 |
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Target: 5'- -uCCCguuuaucCACAagaguCAGGAUCCACCGUg -3' miRNA: 3'- uuGGGauu----GUGU-----GUCCUAGGUGGCGg -5' |
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| 6160 | 3' | -54.3 | NC_001837.1 | + | 115 | 1.1 | 0.000079 |
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Target: 5'- gAACCCUAACACACAGGAUCCACCGCCu -3' miRNA: 3'- -UUGGGAUUGUGUGUCCUAGGUGGCGG- -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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