miRNA: 3'- -UgcCCCGGuGUGGGGUCC---UCCAU-----UGG- -5'
miRNA: 3'- -UGCCC-CGGUG---UGGGGUCcucCAUUGG- -5'
miRNA: 3'- uGCC-CCGG-------UGUGG-GGUCCuCCAUUGG- -5'
miRNA: 3'- -UGCCCCGGUGUGGGgUC-CucCAuUGG- -5'
miRNA: 3'- -UGCCCCGGUGUGGGGUCCUCCAUUGG- -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 | |||||||
| 31936 | 3' | -59.9 | NC_006940.1 | + | 26238 | 0.66 | 0.379004 |
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Target: 5'- uGauGGGCCuCGCCCUGGGgagAGGUGgggacGCCu -3' miRNA: 3'- -UgcCCCGGuGUGGGGUCC---UCCAU-----UGG- -5' |
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| 31936 | 3' | -59.9 | NC_006940.1 | + | 6639 | 0.66 | 0.379004 |
|
Target: 5'- aGCGGGcGUCACaacGCCCUAGc--GUAACCg -3' miRNA: 3'- -UGCCC-CGGUG---UGGGGUCcucCAUUGG- -5' |
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| 31936 | 3' | -59.9 | NC_006940.1 | + | 17570 | 0.7 | 0.225243 |
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Target: 5'- uCGGcGGCUauguccuAUACCgCCGGG-GGUGACCa -3' miRNA: 3'- uGCC-CCGG-------UGUGG-GGUCCuCCAUUGG- -5' |
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| 31936 | 3' | -59.9 | NC_006940.1 | + | 17799 | 0.75 | 0.097239 |
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Target: 5'- gGCGGGGCCGCACCUgGGuGcuGUuACCg -3' miRNA: 3'- -UGCCCCGGUGUGGGgUC-CucCAuUGG- -5' |
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| 31936 | 3' | -59.9 | NC_006940.1 | + | 2094 | 1.11 | 0.000162 |
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Target: 5'- gACGGGGCCACACCCCAGGAGGUAACCg -3' miRNA: 3'- -UGCCCCGGUGUGGGGUCCUCCAUUGG- -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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