miRNA: 3'- -UAAGCCAUGGCCCGGGCUGCUCAUGG- -5'
miRNA: 3'- uaAGcCAUGGCCCGGGCU-GC--UCAUGG- -5'
miRNA: 3'- uaAGCCa---------UGGCCCGGGCUGCUC-AUGG- -5'
miRNA: 3'- -UAAGCCA-------UGGCCCGgGCUGCU------CAUGg -5'
miRNA: 3'- uaaGCCAUG----GCCCGGGCugcuCAUGG- -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 | |||||||
| 11674 | 3' | -56.9 | NC_003102.1 | + | 98512 | 1.1 | 0.001974 |
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Target: 5'- aAUUCGGUACCGGGCCCGACGAGUACCg -3' miRNA: 3'- -UAAGCCAUGGCCCGGGCUGCUCAUGG- -5' |
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| 11674 | 3' | -56.9 | NC_003102.1 | + | 95483 | 0.69 | 0.704807 |
|
Target: 5'- -gUC-GUGCCGGGUCCGGuCGucGGUAUCg -3' miRNA: 3'- uaAGcCAUGGCCCGGGCU-GC--UCAUGG- -5' |
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| 11674 | 3' | -56.9 | NC_003102.1 | + | 4391 | 0.67 | 0.825571 |
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Target: 5'- -aUCGGgcugcuguucAUCGGGUUCGACGGGcUGCUg -3' miRNA: 3'- uaAGCCa---------UGGCCCGGGCUGCUC-AUGG- -5' |
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| 11674 | 3' | -56.9 | NC_003102.1 | + | 6388 | 0.66 | 0.864516 |
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Target: 5'- uGUUCGGUcuuuuauAUCGGGCgCGAUGAcaguguGUGCg -3' miRNA: 3'- -UAAGCCA-------UGGCCCGgGCUGCU------CAUGg -5' |
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| 11674 | 3' | -56.9 | NC_003102.1 | + | 98346 | 0.66 | 0.865261 |
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Target: 5'- --aCGGUACucguCGGGCCCG----GUACCg -3' miRNA: 3'- uaaGCCAUG----GCCCGGGCugcuCAUGG- -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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