. 2006 Nov 29;7(11):R112. doi: 10.1186/gb-2006-7-11-r112

Table 2.

Regions with extreme TE density in the D. melanogaster Release 4 genome sequence

HDR	Chromosome	Start	End	No. of families	No. of TEs	No. nested	Duplicated TEs	Collinear	Genes
1	X	19,744,508	19,790,060	7	22	0	+	+	2 (8)
2	X	20,958,143	20,988,686	13	18	2	+	+	1
3*	X	21,332,555	21,366,773	13	14	13	-	+	0
4^†	X	21,434,542	21,663,556	42	104	39	+	+	6
5	X	21,726,082	21,780,371	10	12	4	-	+	5
6	X	21,883,728	21,974,732	16	21	0	-	+	0
7	X	22,085,438	22,224,390	19	38	12	+	Base	9
8	2L	20,100,865	20,210,447	27	61	18	+	+	1
9^‡§	2L	21,312,749	21,403,782	20	29	6	+	+	7 (3)
10^‡§	2L	21,527,053	21,725,165	36	55	17	-	+	10 (1)
11	2L	22,064,386	22,407,834	61	157	52	+	Base	19 (1)
12*	2R	387	1,185,590	103	571	156	+	Base	45
13^§	2R	1,744,145	2,011,104	42	92	46	+	-	2
14	3L	22,910,473	23,771,865	91	411	128	+	Base	17
15	3R	310,015	436,430	22	37	8	-	+	9
16*	3R	8,294,200	8,327,684	5	38	33	+	+	1
17	3R	27,888,358	27,905,053	2	20	12	+	Tip	1
18	4	1	46,860	12	14	4	-	Base	2 (2)
19	4	201,177	269,428	10	16	9	-	+	6
20	4	303,028	348,412	7	10	2	-	+	4
21	4	433,967	496,527	10	20	7	+	+	4
22	4	926,385	997,041	12	18	3	-	+	5
23	4	1,163,173	1,281,586	18	44	13	-	Tip	9

HDRs were defined as having >10 non-INE-1 TEs in a 50 Kb window. Numbers of distinct families, numbers of TEs, number of TEs involved in nests, and the presence of duplicated TEs all exclude INE-1. A plus indicates that unique sequences flanking a HDR are in the collinear orientation in the D. yakuba genome. Orthologous regions could not be obtained for both flanking regions for HDRs at the tip or base of chromosome arms. Numbers of genes include coding and non-coding genes, with numbers of pseudogenes indicated in parentheses. *Likely to be fixed in D. melanogaster. ^†Physical gap present in HDR. ^‡HDRs 9 and 10 flank the Histone gene cluster and likely represent a single HDR. ^§'Weak points' in polytene chromosomes.