Table 1: Genomatrix Analysis of STAT Consensus Sequence

HIV-LTR Subtype Core Sequence Similarity* Matrix Sequence Similarity**
A 0.758 0.874
B 1 0.742
C 1 0.768
D 1 0.742
E (CRF01-AE) 0.758 0.874
F Under threshold Under threshold
G 1 1
G” (CRF02-AG) 1 0.761

* Defined as the consecutive (usually 4) highest conserved positions of the matrix. The maximum core similarity of 1.0 is only reached when the highest conserved bases of a matrix match exactly in the sequence.
** Defined as the entire sequence of the putative DNA binding site. A perfect match to the matrix is indicated by a score of 1.0 (each sequence position corresponds to the highest conserved nucleotide at that position in the matrix), a statistically significant match to the matrix must show a similarity of >0.8.