miRNA: 3'- uACGg-GAGcAGCGGCUCCC--------------UCGGCaa -5'
miRNA: 3'- uACGGG-AGC---------------AGCGGCUCCC----UCGGcaa -5'
miRNA: 3'- uaCGGGAGc-------AGCGGCUCCC-----UCGGCAa -5'
miRNA: 3'- -UACGGGAGCAGCGGCUCCCUCGGCAA- -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 | |||||||
| 30452 | 5' | -62.6 | NC_006548.1 | + | 23493 | 0.66 | 0.249766 |
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Target: 5'- cUGCagCUCaUCGCCGAGGGcaaguucagccucgGGCCGg- -3' miRNA: 3'- uACGg-GAGcAGCGGCUCCC--------------UCGGCaa -5' |
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| 30452 | 5' | -62.6 | NC_006548.1 | + | 20845 | 0.68 | 0.180776 |
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Target: 5'- cUGCCCgUCGacaccccccuggaguUCGCCGAGGGcgacGGCCa-- -3' miRNA: 3'- uACGGG-AGC---------------AGCGGCUCCC----UCGGcaa -5' |
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| 30452 | 5' | -62.6 | NC_006548.1 | + | 17408 | 0.69 | 0.151994 |
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Target: 5'- -cGCCUUCcaccgaguUCGCCGAGGGcgaucAGCCGUc -3' miRNA: 3'- uaCGGGAGc-------AGCGGCUCCC-----UCGGCAa -5' |
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| 30452 | 5' | -62.6 | NC_006548.1 | + | 22133 | 1.03 | 0.000269 |
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Target: 5'- cAUGCCCUCGUCGCCGAGGGAGCCGUUa -3' miRNA: 3'- -UACGGGAGCAGCGGCUCCCUCGGCAA- -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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