miRNA: 3'- uaUUUCCCUGa-CCAUAGAGagCGGuu -5'
miRNA: 3'- uauUUCCCUga-CCAUAG--------------AGAGCGGUU- -5'
miRNA: 3'- uauUUCCCugAC-CAUAGAGAG------CGGUu -5'
miRNA: 3'- uauUUCCCugAC-CAUAGAGAG------CGGUu -5'
miRNA: 3'- -UAUUUCCCUGACCAUAGAGAGCGGUU- -5'
Results 1 - 5 of 5 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 | |||||||
| 3085 | 5' | -51.6 | NC_001493.1 | + | 44199 | 0.67 | 0.946827 |
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Target: 5'- -aAGAGGGGCcgGGUAUUUCggGCCc- -3' miRNA: 3'- uaUUUCCCUGa-CCAUAGAGagCGGuu -5' |
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| 3085 | 5' | -51.6 | NC_001493.1 | + | 20959 | 0.68 | 0.905901 |
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Target: 5'- --cGAGGGAgagGGUAUCgagcaauucgcgacUCUCGCCGAg -3' miRNA: 3'- uauUUCCCUga-CCAUAG--------------AGAGCGGUU- -5' |
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| 3085 | 5' | -51.6 | NC_001493.1 | + | 132681 | 0.71 | 0.802524 |
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Target: 5'- --uGAGGGugUGuGUGUCUCUCcguauaGCCAc -3' miRNA: 3'- uauUUCCCugAC-CAUAGAGAG------CGGUu -5' |
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| 3085 | 5' | -51.6 | NC_001493.1 | + | 17127 | 0.71 | 0.802524 |
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Target: 5'- --uGAGGGugUGuGUGUCUCUCcguauaGCCAc -3' miRNA: 3'- uauUUCCCugAC-CAUAGAGAG------CGGUu -5' |
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| 3085 | 5' | -51.6 | NC_001493.1 | + | 68182 | 1.05 | 0.009582 |
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Target: 5'- cAUAAAGGGACUGGUAUCUCUCGCCAAg -3' miRNA: 3'- -UAUUUCCCUGACCAUAGAGAGCGGUU- -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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