miRNA: 3'- -CCGUU------UGCU-GCGGGugC----AugCCAGGu -5'
miRNA: 3'- -CCGuUUGCugCGGGugCA--UGCC---AGGU- -5'
miRNA: 3'- cCGUUUGC-----UGCGGGUGcaUGCCAGGU- -5'
miRNA: 3'- cCGuuUGCUGCg--GGUGCaUGCCAGGU- -5'
miRNA: 3'- -CCGUUUGCUGCGGGUGCAUGCCAGGU- -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 | |||||||
| 4283 | 3' | -54.9 | NC_001710.1 | + | 1804 | 0.66 | 0.245957 |
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Target: 5'- aGGCAAcccgguGCGGuCGCCCuuGgguuUugGGUCCu -3' miRNA: 3'- -CCGUU------UGCU-GCGGGugC----AugCCAGGu -5' |
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| 4283 | 3' | -54.9 | NC_001710.1 | + | 7441 | 0.67 | 0.231861 |
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Target: 5'- uGGCcGGCGugGCCCuaGUcaGCGGcacUCCAg -3' miRNA: 3'- -CCGuUUGCugCGGGugCA--UGCC---AGGU- -5' |
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| 4283 | 3' | -54.9 | NC_001710.1 | + | 6620 | 0.7 | 0.14211 |
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Target: 5'- cGCGGACGcucguGCGCCCGCc-AUGGUCUAu -3' miRNA: 3'- cCGUUUGC-----UGCGGGUGcaUGCCAGGU- -5' |
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| 4283 | 3' | -54.9 | NC_001710.1 | + | 208 | 0.75 | 0.057555 |
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Target: 5'- uGCcuGCGGCGagaCCGCGcACGGUCCAc -3' miRNA: 3'- cCGuuUGCUGCg--GGUGCaUGCCAGGU- -5' |
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| 4283 | 3' | -54.9 | NC_001710.1 | + | 310 | 1.1 | 0.000079 |
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Target: 5'- gGGCAAACGACGCCCACGUACGGUCCAc -3' miRNA: 3'- -CCGUUUGCUGCGGGUGCAUGCCAGGU- -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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