| Protein | NCBI GeneID | Class | Sub class | Motif | Logo |
| HOXB9 | 3219 | TF | Homeobox | 29 |  |
| HHEX | 3087 | TF | Homeobox | 26 |  |
| MEIS3 | 56917 | TF | Homeobox | 23 |  |
| PHOX2A | 401 | TF | Homeobox | 18 |  |
| ZHX3 | 23051 | TF | Homeobox | 17 |  |
| POU3F2 | 5454 | TF | Homeobox | 17 |  |
| NKX2-3 | 159296 | TF | Homeobox | 14 |  |
| PRRX1 | 5396 | TF | Homeobox | 14 |  |
| TGIF1 | 7050 | TF | Homeobox | 12 |  |
| POU4F3 | 5459 | TF | Homeobox | 10 |  |
| EVX1 | 2128 | TF | Homeobox | 10 |  |
| HOXD3 | 3232 | TF | Homeobox | 9 |  |
| DLX6 | 1750 | TF | Homeobox | 9 |  |
| VAX2 | 25806 | TF | Homeobox | 7 |  |
| HOXB13 | 10481 | TF | Homeobox | 7 |  |
| LHX2 | 9355 | TF | Homeobox | 5 |  |
| ESX1 | 80712 | TF | Homeobox | 5 |  |
| PITX1 | 5307 | TF | Homeobox | 5 |  |
| BARX1 | 56033 | TF | Homeobox | 5 |  |
| PKNOX2 | 63876 | TF | Homeobox | 5 |  |
| LHX4 | 89884 | TF | Homeobox | 4 |  |
| TGIF2LX | 90316 | TF | Homeobox | 3 |  |
| POU6F1 | 5463 | TF | Homeobox | 130 | |
| ISL1 | 3670 | TF | Homeobox | 66 | |
| PBX2 | 5089 | TF | Homeobox | 56 | |
| PKNOX1 | 5316 | TF | Homeobox | 53 | |
| MEIS2 | 4212 | TF | Homeobox | 37 | |
| OTX2 | 5015 | TF | Homeobox | 33 | |
| MEIS1 | 4211 | TF | Homeobox | 2 | |
| PROP1 | 5626 | TF | Homeobox | 1 | |
| SIX1 | 6495 | TF | Homeobox | 1 | |
| NKX2-5 | 1482 | TF | Homeobox | 1 | |
| IRX2 | 153572 | TF | Homeobox | 1 | |
| IRX5 | 10265 | TF | Homeobox | 1 | |
| HOXC8 | 3224 | TF | Homeobox | 1 | |
| HOXD8 | 3234 | TF | Homeobox | 1 | |
| HOXB1 | 3211 | TF | Homeobox | 1 | |
| SIX2 | 10736 | TF | Homeobox | 1 | |
| BARX2 | 8538 | TF | Homeobox | 1 |
We calculated the consensus sequences for the proteins with number of binding motifs between 3 and 29.
The proteins with more than 30 binding motifs are considered as either non specific or binding to T7 promoter