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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 | |||||||
| 12437 | 3' | -55.1 | NC_003324.1 | + | 50378 | 0.66 | 0.754832 |
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Target: 5'- -aAGUGCCGUCGCcguugUCcCGGg-CCGCg -3' miRNA: 3'- gcUCACGGCAGUGa----AGcGCCaaGGUG- -5' |
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| 12437 | 3' | -55.1 | NC_003324.1 | + | 57178 | 0.66 | 0.754832 |
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Target: 5'- aGGGccUGCCGcUCACagacaagcgcCGUGGUUCCAUg -3' miRNA: 3'- gCUC--ACGGC-AGUGaa--------GCGCCAAGGUG- -5' |
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| 12437 | 3' | -55.1 | NC_003324.1 | + | 27352 | 0.66 | 0.734074 |
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Target: 5'- aGGGUugugGCCGUCGCU--GCGGUacuucgugccgUCUACa -3' miRNA: 3'- gCUCA----CGGCAGUGAagCGCCA-----------AGGUG- -5' |
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| 12437 | 3' | -55.1 | NC_003324.1 | + | 8594 | 0.66 | 0.71291 |
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Target: 5'- cCGAGgacCgCGUCACgggCGCGGUUUCGa -3' miRNA: 3'- -GCUCac-G-GCAGUGaa-GCGCCAAGGUg -5' |
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| 12437 | 3' | -55.1 | NC_003324.1 | + | 36445 | 0.69 | 0.571471 |
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Target: 5'- aGGGcaUGCCGUCGCgccCGCGGcgcuugUUCCAg -3' miRNA: 3'- gCUC--ACGGCAGUGaa-GCGCC------AAGGUg -5' |
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| 12437 | 3' | -55.1 | NC_003324.1 | + | 49773 | 0.7 | 0.497401 |
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Target: 5'- -aAGUGCCGUCggggAUUUCGCGGUUUUc- -3' miRNA: 3'- gcUCACGGCAG----UGAAGCGCCAAGGug -5' |
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| 12437 | 3' | -55.1 | NC_003324.1 | + | 26289 | 0.72 | 0.399982 |
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Target: 5'- uCGAGcUGgC-UCACUUCGCGGUacgucuguUCCGCg -3' miRNA: 3'- -GCUC-ACgGcAGUGAAGCGCCA--------AGGUG- -5' |
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| 12437 | 3' | -55.1 | NC_003324.1 | + | 18054 | 1.1 | 0.000926 |
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Target: 5'- gCGAGUGCCGUCACUUCGCGGUUCCACa -3' miRNA: 3'- -GCUCACGGCAGUGAAGCGCCAAGGUG- -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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