Repeat Table

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Repeat Table for Human Herpesvirus 2 HG52

The tandem repeats listed in the table were identified using the Tandem Repeat Finder by G. Genson
"Tandem repeats finder: a program to analyze DNA sequences" Nucleic Acids Research (1999) Vol. 27, No. 2, pp. 573-580.

Repeat Name Copy # Location Length Gene & Intergenic Id(s) Definitions-Comments
LTR a 3.00 1,254
126996,127249
154493,154746 IGR1, IGR50, IGR63 Bases 1-254 of this IGR form the "a" segment of a long terminal repeat. The inverted segment, "a'", is located at genome coordinates 126,996-127,249 and the last 254 bases of the genome are a direct repeat of "a".
Bases 126,996-127,249 are the inverted, internal "a'" segment of a long termainal repeat of form a...........a'...a This region contains three tandem nucleotide repeats with genome coordinates: 1) 127173 - 127237 with period(unit size) 28, copy # 2.3, 83% matches and no inserts/deletes. 2) 127455 - 127490 with period(unit size) 15, copy # 2.4, 100% matches and no inserts/deletes. 3) 127672 - 127914 with period(unit size) 15, copy # 16.2, 100% matches and no inserts/deletes.
intergenic region [Bases 154,493 - 154,746 (ie the last 254 bases of the genome) are the direct "a" segment of the long terminal repeat of form a..........a'...a This region contains two tandem nucleotide repeats at genome coordinates: 1) 153828 - 154070 with period(unit size) 15, copy # 16.2, 100% matches and no inserts/deletes and 2) 154252 - 154287 with period(unit size) 15, copy # 2.4, 100% matches and no inserts/deletes.]
LTR b 2.00 255,9264
117986,126995 HHVTW001 , HHVTW002 , HHVTW001.1 , IGR1, IGR2, IGR1.1, HHVTW061 , HHVTW062 , HHVTW061.1 , IGR48, IGR49, IGR50 anti-host defense factor, ICP34.5 (RL1_HSV2H)
promiscuous transactivator, cellular homolog, ICP0, VMW118 (ICP0_HSV2H)
unknown
Bases 1-254 of this IGR form the "a" segment of a long terminal repeat. The inverted segment, "a'", is located at genome coordinates 126,996-127,249 and the last 254 bases of the genome are a direct repeat of "a".
This region contains five tandem nucleotide repeats with genome coordinates: 1) 6394-6427, period/unit size 15, copy # 2.3, with 94% matches and no insert/deletes. 2) 7990-8042, period/unit size 19, copy # 2.7, with 97% matches and one insert/detete. 3) 8247-8271, period/unit size 2, copy # 12.5 with 100% matches and no insert/deletes. 4) 9043-9193, period/unit size 21, copy # 7.2 with 99% matches and no insets/deletes. 5) 9242-9297, period/unit size 17, copy # 3.3 with 100% matches and no insert/deletes.
This region contains one tandem nucleotide repeat with genomic coordinates 1635-1730, period/unit size 40, copy # 2.4, with 82% matches and no inserts/deletes.
promiscuous transactivator, cellular homolog, VMW118, ICP0
anti-host defense factor, ICP34.5 (RL1_HSV2H)
unknown
intergenic region [This region contains four tandem nucleotide repeats at genome coordinates: 1) 118057 - 118207 with period/unit size 21, copy # 7.2, 99% matches and no inserts/deletes. 2) 118979 - 119003 with perios/unit size 2, copy # 12.5, 100% matches, and no inserts/deletes. 3) 119208 - 119260 with period/unit size 19, copy # 2.7, 97% matches and one insert/delete. 4) 120823 - 120856 with period/unit size 15, copy # 2.3, 94% matches and no inserts/deletes. ]
intergenic region [This region contains one tandem nucleotide repeat at genome coordinates 125509 - 125615 with period(unit size) 40, copy # 2.7, 80% matches and no inserts/deletes.]
intergenic region [Bases 126,996-127,249 are the inverted, internal "a'" segment of a long termainal repeat of form a...........a'...a This region contains three tandem nucleotide repeats with genome coordinates: 1) 127173 - 127237 with period(unit size) 28, copy # 2.3, 83% matches and no inserts/deletes. 2) 127455 - 127490 with period(unit size) 15, copy # 2.4, 100% matches and no inserts/deletes. 3) 127672 - 127914 with period(unit size) 15, copy # 16.2, 100% matches and no inserts/deletes.]
LTR c 2.00 127250,133706
148036,154492 HHVTW063 , IGR50, IGR51, HHVTW077 , IGR63, IGR62 positive and negative gene regulator, ICP4
Bases 126,996-127,249 are the inverted, internal "a'" segment of a long termainal repeat of form a...........a'...a This region contains three tandem nucleotide repeats with genome coordinates: 1) 127173 - 127237 with period(unit size) 28, copy # 2.3, 83% matches and no inserts/deletes. 2) 127455 - 127490 with period(unit size) 15, copy # 2.4, 100% matches and no inserts/deletes. 3) 127672 - 127914 with period(unit size) 15, copy # 16.2, 100% matches and no inserts/deletes.
positive and negative gene regulator, ICP4
intergenic region [Bases 154,493 - 154,746 (ie the last 254 bases of the genome) are the direct "a" segment of the long terminal repeat of form a..........a'...a This region contains two tandem nucleotide repeats at genome coordinates: 1) 153828 - 154070 with period(unit size) 15, copy # 16.2, 100% matches and no inserts/deletes and 2) 154252 - 154287 with period(unit size) 15, copy # 2.4, 100% matches and no inserts/deletes.]
intergenic region [This region contains three tandem nucleotide repeats at genome coordinates: 1) 148097 - 148366 with period(unit size) 8, copy # 35.6, 85% matches and 28 inserts/deletes. 2) 148098 - 148483 with period(unit size) 16, copy # 28.9, 85% matches and 60 inserts/deletes. 3) 148832 - 149119 with period(unit size) 138, copy # 2.1 98% matches and 3 inserts/deletes.]

Los Alamos National Laboratory • Est 1943

Repeat Name	Copy #	Location	Length	Gene & Intergenic Id(s)	Definitions-Comments
LTR a	3.00	1,254 126996,127249 154493,154746		IGR1, IGR50, IGR63	Bases 1-254 of this IGR form the "a" segment of a long terminal repeat. The inverted segment, "a'", is located at genome coordinates 126,996-127,249 and the last 254 bases of the genome are a direct repeat of "a". Bases 126,996-127,249 are the inverted, internal "a'" segment of a long termainal repeat of form a...........a'...a This region contains three tandem nucleotide repeats with genome coordinates: 1) 127173 - 127237 with period(unit size) 28, copy # 2.3, 83% matches and no inserts/deletes. 2) 127455 - 127490 with period(unit size) 15, copy # 2.4, 100% matches and no inserts/deletes. 3) 127672 - 127914 with period(unit size) 15, copy # 16.2, 100% matches and no inserts/deletes. intergenic region [Bases 154,493 - 154,746 (ie the last 254 bases of the genome) are the direct "a" segment of the long terminal repeat of form a..........a'...a This region contains two tandem nucleotide repeats at genome coordinates: 1) 153828 - 154070 with period(unit size) 15, copy # 16.2, 100% matches and no inserts/deletes and 2) 154252 - 154287 with period(unit size) 15, copy # 2.4, 100% matches and no inserts/deletes.]
LTR b	2.00	255,9264 117986,126995		HHVTW001 , HHVTW002 , HHVTW001.1 , IGR1, IGR2, IGR1.1, HHVTW061 , HHVTW062 , HHVTW061.1 , IGR48, IGR49, IGR50	anti-host defense factor, ICP34.5 (RL1_HSV2H) promiscuous transactivator, cellular homolog, ICP0, VMW118 (ICP0_HSV2H) unknown Bases 1-254 of this IGR form the "a" segment of a long terminal repeat. The inverted segment, "a'", is located at genome coordinates 126,996-127,249 and the last 254 bases of the genome are a direct repeat of "a". This region contains five tandem nucleotide repeats with genome coordinates: 1) 6394-6427, period/unit size 15, copy # 2.3, with 94% matches and no insert/deletes. 2) 7990-8042, period/unit size 19, copy # 2.7, with 97% matches and one insert/detete. 3) 8247-8271, period/unit size 2, copy # 12.5 with 100% matches and no insert/deletes. 4) 9043-9193, period/unit size 21, copy # 7.2 with 99% matches and no insets/deletes. 5) 9242-9297, period/unit size 17, copy # 3.3 with 100% matches and no insert/deletes. This region contains one tandem nucleotide repeat with genomic coordinates 1635-1730, period/unit size 40, copy # 2.4, with 82% matches and no inserts/deletes. promiscuous transactivator, cellular homolog, VMW118, ICP0 anti-host defense factor, ICP34.5 (RL1_HSV2H) unknown intergenic region [This region contains four tandem nucleotide repeats at genome coordinates: 1) 118057 - 118207 with period/unit size 21, copy # 7.2, 99% matches and no inserts/deletes. 2) 118979 - 119003 with perios/unit size 2, copy # 12.5, 100% matches, and no inserts/deletes. 3) 119208 - 119260 with period/unit size 19, copy # 2.7, 97% matches and one insert/delete. 4) 120823 - 120856 with period/unit size 15, copy # 2.3, 94% matches and no inserts/deletes. ] intergenic region [This region contains one tandem nucleotide repeat at genome coordinates 125509 - 125615 with period(unit size) 40, copy # 2.7, 80% matches and no inserts/deletes.] intergenic region [Bases 126,996-127,249 are the inverted, internal "a'" segment of a long termainal repeat of form a...........a'...a This region contains three tandem nucleotide repeats with genome coordinates: 1) 127173 - 127237 with period(unit size) 28, copy # 2.3, 83% matches and no inserts/deletes. 2) 127455 - 127490 with period(unit size) 15, copy # 2.4, 100% matches and no inserts/deletes. 3) 127672 - 127914 with period(unit size) 15, copy # 16.2, 100% matches and no inserts/deletes.]
LTR c	2.00	127250,133706 148036,154492		HHVTW063 , IGR50, IGR51, HHVTW077 , IGR63, IGR62	positive and negative gene regulator, ICP4 Bases 126,996-127,249 are the inverted, internal "a'" segment of a long termainal repeat of form a...........a'...a This region contains three tandem nucleotide repeats with genome coordinates: 1) 127173 - 127237 with period(unit size) 28, copy # 2.3, 83% matches and no inserts/deletes. 2) 127455 - 127490 with period(unit size) 15, copy # 2.4, 100% matches and no inserts/deletes. 3) 127672 - 127914 with period(unit size) 15, copy # 16.2, 100% matches and no inserts/deletes. positive and negative gene regulator, ICP4 intergenic region [Bases 154,493 - 154,746 (ie the last 254 bases of the genome) are the direct "a" segment of the long terminal repeat of form a..........a'...a This region contains two tandem nucleotide repeats at genome coordinates: 1) 153828 - 154070 with period(unit size) 15, copy # 16.2, 100% matches and no inserts/deletes and 2) 154252 - 154287 with period(unit size) 15, copy # 2.4, 100% matches and no inserts/deletes.] intergenic region [This region contains three tandem nucleotide repeats at genome coordinates: 1) 148097 - 148366 with period(unit size) 8, copy # 35.6, 85% matches and 28 inserts/deletes. 2) 148098 - 148483 with period(unit size) 16, copy # 28.9, 85% matches and 60 inserts/deletes. 3) 148832 - 149119 with period(unit size) 138, copy # 2.1 98% matches and 3 inserts/deletes.]