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Table 1.

IR-1 Elements inC. elegans

Element no.	Chromosome	Location	Nearest Gene(s)	Size (bp)	Comment	Percent Identity	TSD (bp)	TSD
R07D5	X	intergenic	unc-7, R07D5.2	379	full length	99.5	2	AT
F18E3	V	intergenic	F18E3.1 F18E3.2	379	full length	99.2	2	TA
F08G5	IV	intron	F08G5.5	379	full length	97.4	2	TA
C17C3	II	intron	C17C3.12	379	full length	96.6	2	AA
F39B3	X	intergenic	F39B3, Unknown	400	internal insertion	96.0	2	AA
C04E47	X	intergenic	C04E7.2, C04E7.3	379	full length	94.5	2	AC
F52H3	II	intergenic	ZK892.5 F52H3.7	399	truncated, unique spacer	70.0	2	AT^*
F35E12	V	—	—	392	internal insertion	94.4	2	AC
F22B7	III	intergenic	F22B7.9, F22B7.10	194	truncated	97.5	2	TT^*
ZK849	I	—	—	1105	internal insertion	—	2	TA
F47E1	X	intron	F47E1.3	112	truncated and rearranged	82.1	2	TA^*
ZC8	X	intergenic	ZC8.2, ZC8.3	1105	internal insertion	—	2	TA
F54D1	IV	intergenic	F54D1.5, F54D1.6	1083	internal insertion	—	none
F45E1	X	intron	F45E1.7	103	internal deletion	99.0	2	CA
F10D11	I	intron	F10D11.d	173	internal deletion	—	2	TA
ZK354	I	—	—	173	internal deletion	—	2	TA
F02E9	I	—	—	173	internal deletion	—	2	TA
C44H4	X	intron	C44H4.6	102	internal deletion	—	2	TG
DH11	II	intergenic	DH11.1, DH11.2	84	internal deletion	100	2	TA

[i] Copies of IR-1 found in the C. elegans genome. Of the 19 elements shown, 14 had BLAST P < 10⁻²⁵, using the consensus element sequence as the query (Table 2). The remaining five elements (at the bottom) had BLAST P < 10⁻¹⁹. The element number is the same as the corresponding cosmid number for the clone harboring the element. Elements were classified as intergenic if they were between known or predicted genes, or as intron if located within the intron of a known or predicted gene. Percent identity is relative to the reference consensus sequence (Table2). An asterisk (*) next to the target site duplication (TSD) indicates that the element was truncated at one end, and the intact end was used to determine the expected duplication sequence. Elements within regions for which information is not yet available have dashes in the appropriate column. Similar tables are available at our website for this and the other element families (http://www.welch.jhu.edu/~devine/RepDNAdb.html). In the website tables, the element number is hot-linked to the appropriate GenBank record, facilitating rapid information retrieval.