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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 | |||||||
| 28879 | 3' | -48.5 | NC_006146.1 | + | 50776 | 0.66 | 0.998526 |
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Target: 5'- -cGCUCUCCucGGUGguGugGGCacACGg -3' miRNA: 3'- uaUGAGAGG--UCACguCugUUGauUGU- -5' |
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| 28879 | 3' | -48.5 | NC_006146.1 | + | 84878 | 0.67 | 0.997854 |
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Target: 5'- -aGCggCUCCAGUgGCAG-CGacACUGGCAa -3' miRNA: 3'- uaUGa-GAGGUCA-CGUCuGU--UGAUUGU- -5' |
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| 28879 | 3' | -48.5 | NC_006146.1 | + | 107132 | 0.67 | 0.997854 |
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Target: 5'- --cCUCUCCAacGUGCAGAUAGgCUAc-- -3' miRNA: 3'- uauGAGAGGU--CACGUCUGUU-GAUugu -5' |
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| 28879 | 3' | -48.5 | NC_006146.1 | + | 102191 | 0.67 | 0.996378 |
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Target: 5'- -aGCUCUCgGGgacGCGGACGGCgu-CAa -3' miRNA: 3'- uaUGAGAGgUCa--CGUCUGUUGauuGU- -5' |
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| 28879 | 3' | -48.5 | NC_006146.1 | + | 95063 | 0.68 | 0.994153 |
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Target: 5'- -gGCUC-CCAcucGUGguGGCAGCUGugGu -3' miRNA: 3'- uaUGAGaGGU---CACguCUGUUGAUugU- -5' |
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| 28879 | 3' | -48.5 | NC_006146.1 | + | 31443 | 0.71 | 0.955163 |
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Target: 5'- --cUUCUCCAGUGCAGGCAcccccccgGGCAc -3' miRNA: 3'- uauGAGAGGUCACGUCUGUuga-----UUGU- -5' |
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| 28879 | 3' | -48.5 | NC_006146.1 | + | 30384 | 1.08 | 0.016599 |
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Target: 5'- aAUACUCUCCAGUGCAGACAACUAACAa -3' miRNA: 3'- -UAUGAGAGGUCACGUCUGUUGAUUGU- -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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