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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 | |||||||
| 396 | 3' | -55.2 | AC_000011.1 | + | 12995 | 0.66 | 0.606901 |
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Target: 5'- gAGCGUG-GGCCuGUUcCUGAUGCaGGAg -3' miRNA: 3'- -UCGCGCaCUGG-CAAuGACUGCGgUCU- -5' |
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| 396 | 3' | -55.2 | AC_000011.1 | + | 11873 | 0.66 | 0.606901 |
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Target: 5'- gGGCGCG-GACCugcACUGGCagcccagccGCCGGGc -3' miRNA: 3'- -UCGCGCaCUGGcaaUGACUG---------CGGUCU- -5' |
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| 396 | 3' | -55.2 | AC_000011.1 | + | 31322 | 0.66 | 0.605769 |
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Target: 5'- uAGUGCGUGugCcugagGUUGCUGugGUgguguguCAGGu -3' miRNA: 3'- -UCGCGCACugG-----CAAUGACugCG-------GUCU- -5' |
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| 396 | 3' | -55.2 | AC_000011.1 | + | 9852 | 0.71 | 0.308568 |
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Target: 5'- uGCGCGUGagcccgaagccgcGCUGggGCUGgacgaGCGCCAGGu -3' miRNA: 3'- uCGCGCAC-------------UGGCaaUGAC-----UGCGGUCU- -5' |
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| 396 | 3' | -55.2 | AC_000011.1 | + | 15967 | 0.71 | 0.301548 |
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Target: 5'- cGCGCGUcuccggguccuGCCGgcGCUGGCGCCuGAa -3' miRNA: 3'- uCGCGCAc----------UGGCaaUGACUGCGGuCU- -5' |
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| 396 | 3' | -55.2 | AC_000011.1 | + | 15372 | 1.09 | 0.000644 |
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Target: 5'- cAGCGCGUGACCGUUACUGACGCCAGAc -3' miRNA: 3'- -UCGCGCACUGGCAAUGACUGCGGUCU- -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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