Heterogeneity of Signal Transducer and Activator of Transcription Binding Sites in the Long-Terminal Repeats of Distinct HIV-1 Subtypes

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.