miRNA: 3'- -UAGCUUGU-CAGCGGCuGUAccAUGAG- -5'
miRNA: 3'- uAGCUUGUC-AGCGGCUG----------UaCCAugAG- -5'
miRNA: 3'- uaGCUUGuCAGCGGCUguaCCAUGAg -5'
miRNA: 3'- -UAGCUugU-------------CAGCGGC-UGUACCAUGag -5'
miRNA: 3'- -UAGCUUGUCAGCGGCUGUACCAUGAG- -5'
Results 1 - 5 of 5 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 | |||||||
| 12699 | 5' | -52.3 | NC_003349.1 | + | 19255 | 0.66 | 0.964125 |
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Target: 5'- gAUCGAGCGuGUCGCUGuCGU--UGCUCu -3' miRNA: 3'- -UAGCUUGU-CAGCGGCuGUAccAUGAG- -5' |
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| 12699 | 5' | -52.3 | NC_003349.1 | + | 28480 | 0.67 | 0.952657 |
|
Target: 5'- uUCGAACAGuUCGUCGAUcacgagaaauAcGGUugUCg -3' miRNA: 3'- uAGCUUGUC-AGCGGCUG----------UaCCAugAG- -5' |
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| 12699 | 5' | -52.3 | NC_003349.1 | + | 126585 | 0.68 | 0.922929 |
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Target: 5'- -aCGAACuGUUGCCGGac-GGUACUa -3' miRNA: 3'- uaGCUUGuCAGCGGCUguaCCAUGAg -5' |
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| 12699 | 5' | -52.3 | NC_003349.1 | + | 68517 | 0.72 | 0.740742 |
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Target: 5'- cGUCGGugAuguacguguauccGUCGCCGaACAUGGUACa- -3' miRNA: 3'- -UAGCUugU-------------CAGCGGC-UGUACCAUGag -5' |
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| 12699 | 5' | -52.3 | NC_003349.1 | + | 19199 | 1.09 | 0.005145 |
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Target: 5'- gAUCGAACAGUCGCCGACAUGGUACUCa -3' miRNA: 3'- -UAGCUUGUCAGCGGCUGUACCAUGAG- -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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