miRNA: 3'- gUAGUCGA---------------AUGAGAGGG-GCAcGGCGG- -5'
miRNA: 3'- -GUAGuCGAa---UGA-GAgGGGcACGGCGG- -5'
miRNA: 3'- -GUAGUcGAAUGAG----AGGGGCaCGgCGG- -5'
miRNA: 3'- -GUAGucGAAUGA-GAGgGGCACGGCGG- -5'
miRNA: 3'- -GUAGUCGAAUGAGAGGGGCACGGCGG- -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 | |||||||
| 1009 | 5' | -56 | NC_000924.1 | + | 40200 | 0.66 | 0.72796 |
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Target: 5'- uGUCGGCUauuucaucccgccaaUAUUUUCCCaCGUcCCGUCa -3' miRNA: 3'- gUAGUCGA---------------AUGAGAGGG-GCAcGGCGG- -5' |
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| 1009 | 5' | -56 | NC_000924.1 | + | 24595 | 0.66 | 0.681076 |
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Target: 5'- gCAUC-GCUgaccACUuCUgCCC-UGCCGCCa -3' miRNA: 3'- -GUAGuCGAa---UGA-GAgGGGcACGGCGG- -5' |
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| 1009 | 5' | -56 | NC_000924.1 | + | 13561 | 0.67 | 0.648546 |
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Target: 5'- aUAUCAaUUUGCUUagagUCCCCG-GCgGCCa -3' miRNA: 3'- -GUAGUcGAAUGAG----AGGGGCaCGgCGG- -5' |
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| 1009 | 5' | -56 | NC_000924.1 | + | 3963 | 0.68 | 0.572563 |
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Target: 5'- gCAUCucUUUGCUgCUCgUCGUGCCGCUg -3' miRNA: 3'- -GUAGucGAAUGA-GAGgGGCACGGCGG- -5' |
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| 1009 | 5' | -56 | NC_000924.1 | + | 26088 | 1.11 | 0.000697 |
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Target: 5'- uCAUCAGCUUACUCUCCCCGUGCCGCCu -3' miRNA: 3'- -GUAGUCGAAUGAGAGGGGCACGGCGG- -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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