miRNA: 3'- aCUCU-GGGCUUG-UAGaa--------C-GGGCCAUC- -5'
miRNA: 3'- acUCUGGG---CU---UGUAGa---ACGGGCCAUC- -5'
miRNA: 3'- acUCUGg-GCUu---GUaGAACGGGCCAUC- -5'
miRNA: 3'- -ACUCUGGGCUUGUAGAACGGGCCAUC- -5'
Results 1 - 4 of 4 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 | |||||||
| 17977 | 5' | -53.6 | NC_004665.1 | + | 26963 | 0.66 | 0.707728 |
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Target: 5'- aGAGAgUCCGAGCgAUCcgcucaagggGaCCCGGUAGa -3' miRNA: 3'- aCUCU-GGGCUUG-UAGaa--------C-GGGCCAUC- -5' |
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| 17977 | 5' | -53.6 | NC_004665.1 | + | 28399 | 0.68 | 0.582403 |
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Target: 5'- -uGGACCCucuGAccuACGUUccugUGCCCGGUGGu -3' miRNA: 3'- acUCUGGG---CU---UGUAGa---ACGGGCCAUC- -5' |
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| 17977 | 5' | -53.6 | NC_004665.1 | + | 10564 | 0.69 | 0.483027 |
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Target: 5'- -aGGACagCGAucuuCAcCUUGCCCGGUGGg -3' miRNA: 3'- acUCUGg-GCUu---GUaGAACGGGCCAUC- -5' |
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| 17977 | 5' | -53.6 | NC_004665.1 | + | 12733 | 1.1 | 0.000765 |
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Target: 5'- gUGAGACCCGAACAUCUUGCCCGGUAGg -3' miRNA: 3'- -ACUCUGGGCUUGUAGAACGGGCCAUC- -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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