Repeat Table

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Repeat Table for Human herpesvirus 1 17

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 1,399
125972,126370
151863,152261 HHVONE000 , IGR1, HHVONE060.1 , IGR49, HHVONE078 , IGR62 latency associated transcript, 5' segment
This region contains one tandem nucleotide repeat with genomic coordinates 98-320, period 12, copy # 18.6, with 100% matches and no inserts/deletes.
latency associated transcript, LAT
This region contains three tandem nucleotide repeats at genome coordinates 1) 126051-126273, period 12, copy # 18.6 with 100% matches and no inserts/deletes, 2) 126571-126709, period 16, copy # 8.7 with 99% matches and no inserts/deletes and 3) 126810-127142, period 17, copy # 19.6 with 100% matches and no inserts/deletes.
latency associated transcript, 3' segment
intergenic region [This region contains three tandem nucleotide repeats at genome coordinates 1) 151091-151423, period 17, copy # 19.6 with 100% matches and no inserts/deletes, 2) 151524-151662, period 16, copy # 8.7 with 99% matches and no inserts/deletes and 3) 151960-152182, period 12, copy # 18.6 with 100% matches and no inserts/deletes. ]
LTR b 2.00 400,8786
117585,125971 HHVONE001 , HHVONE002 , HHVONE001.1 , HHVONE001.2 , HHVONE000 , IGR1, IGR2, IGR1.1, HHVONE061 , HHVONE062 , HHVONE061.1 , HHVONE061.2 , HHVONE060.1 , IGR47, IGR48, IGR49 anti-host defense factor, ICP34.5
promiscuous transactivator, cellular homolog, ICP0, VMW110, IE110 (ICP0_HSV11)
unknown
unknown
latency associated transcript, 5' segment
This region contains one tandem nucleotide repeat with genomic coordinates 98-320, period 12, copy # 18.6, with 100% matches and no inserts/deletes.
This region contains four tandem nucleotide repeats with genomic coordinates 1) 5726-5877, period 16, copy # 9.5, with 99% matches and no inserts/deletes, 2) 7903-7928, period 9, copy # 2.9, with 100% matches and no inserts/deletes, 3) 8552-8583, period 5, copy # 6.4, with 100% matches and no inserts/deletes and 4) 9032-9212, period 17, copy # 10.6, with 100% matches and no inserts/deletes.
promiscuous transactivator, cellular homolog, ICP0, VMW110, IE110 (ICP0_HSV11)
anti-host defense factor, ICP34.5
unknown
unknown
latency associated transcript, LAT
intergenic region [This region contains four tandem nucleotide repeats at genome coordinates 1) 117158-117340, period 17, copy # 10.8, with 100% matches and no inserts/deletes, 2) 117788-117819, period 5, copy # 6.4 with 100% matches and no inseerts/deletes, 3) 118443-118468, period 9 copy # 2.9, with 100% matches and no inserts/deletes and 4) 120494-120645, period 16, copy # 9.4 with 99% matches and no inserts/deletes.]
intergenic region
intergenic region [This region contains three tandem nucleotide repeats at genome coordinates 1) 126051-126273, period 12, copy # 18.6 with 100% matches and no inserts/deletes, 2) 126571-126709, period 16, copy # 8.7 with 99% matches and no inserts/deletes and 3) 126810-127142, period 17, copy # 19.6 with 100% matches and no inserts/deletes.]
LTR c 2.00 126371,132413
145820,151862 HHVONE063 , HHVONE060.1 , IGR49, IGR50, HHVONE077 , HHVONE078 , IGR61, IGR62 positive and negative gene regulator, ICP4 (ICP4_HSV11)
latency associated transcript, LAT
This region contains three tandem nucleotide repeats at genome coordinates 1) 126051-126273, period 12, copy # 18.6 with 100% matches and no inserts/deletes, 2) 126571-126709, period 16, copy # 8.7 with 99% matches and no inserts/deletes and 3) 126810-127142, period 17, copy # 19.6 with 100% matches and no inserts/deletes.
This region contains a tandem nucleotide repeat at genome coordinates 132388-132513, period 22, copy # 5.7 with 99% matches and no inserts/deletes.
positive and negative gene regulator, ICP4 (ICP4_HSV11)
latency associated transcript, 3' segment
intergenic region [This region contains one tandem nucleotide repeat at genome coordinates 145676-145845, period 22, copy # 7.7 with 97% matches and no inserts/deletes. ]
intergenic region [This region contains three tandem nucleotide repeats at genome coordinates 1) 151091-151423, period 17, copy # 19.6 with 100% matches and no inserts/deletes, 2) 151524-151662, period 16, copy # 8.7 with 99% matches and no inserts/deletes and 3) 151960-152182, period 12, copy # 18.6 with 100% matches and no inserts/deletes. ]

Los Alamos National Laboratory • Est 1943

Repeat Name	Copy #	Location	Length	Gene & Intergenic Id(s)	Definitions-Comments
LTR a	3.00	1,399 125972,126370 151863,152261		HHVONE000 , IGR1, HHVONE060.1 , IGR49, HHVONE078 , IGR62	latency associated transcript, 5' segment This region contains one tandem nucleotide repeat with genomic coordinates 98-320, period 12, copy # 18.6, with 100% matches and no inserts/deletes. latency associated transcript, LAT This region contains three tandem nucleotide repeats at genome coordinates 1) 126051-126273, period 12, copy # 18.6 with 100% matches and no inserts/deletes, 2) 126571-126709, period 16, copy # 8.7 with 99% matches and no inserts/deletes and 3) 126810-127142, period 17, copy # 19.6 with 100% matches and no inserts/deletes. latency associated transcript, 3' segment intergenic region [This region contains three tandem nucleotide repeats at genome coordinates 1) 151091-151423, period 17, copy # 19.6 with 100% matches and no inserts/deletes, 2) 151524-151662, period 16, copy # 8.7 with 99% matches and no inserts/deletes and 3) 151960-152182, period 12, copy # 18.6 with 100% matches and no inserts/deletes. ]
LTR b	2.00	400,8786 117585,125971		HHVONE001 , HHVONE002 , HHVONE001.1 , HHVONE001.2 , HHVONE000 , IGR1, IGR2, IGR1.1, HHVONE061 , HHVONE062 , HHVONE061.1 , HHVONE061.2 , HHVONE060.1 , IGR47, IGR48, IGR49	anti-host defense factor, ICP34.5 promiscuous transactivator, cellular homolog, ICP0, VMW110, IE110 (ICP0_HSV11) unknown unknown latency associated transcript, 5' segment This region contains one tandem nucleotide repeat with genomic coordinates 98-320, period 12, copy # 18.6, with 100% matches and no inserts/deletes. This region contains four tandem nucleotide repeats with genomic coordinates 1) 5726-5877, period 16, copy # 9.5, with 99% matches and no inserts/deletes, 2) 7903-7928, period 9, copy # 2.9, with 100% matches and no inserts/deletes, 3) 8552-8583, period 5, copy # 6.4, with 100% matches and no inserts/deletes and 4) 9032-9212, period 17, copy # 10.6, with 100% matches and no inserts/deletes. promiscuous transactivator, cellular homolog, ICP0, VMW110, IE110 (ICP0_HSV11) anti-host defense factor, ICP34.5 unknown unknown latency associated transcript, LAT intergenic region [This region contains four tandem nucleotide repeats at genome coordinates 1) 117158-117340, period 17, copy # 10.8, with 100% matches and no inserts/deletes, 2) 117788-117819, period 5, copy # 6.4 with 100% matches and no inseerts/deletes, 3) 118443-118468, period 9 copy # 2.9, with 100% matches and no inserts/deletes and 4) 120494-120645, period 16, copy # 9.4 with 99% matches and no inserts/deletes.] intergenic region intergenic region [This region contains three tandem nucleotide repeats at genome coordinates 1) 126051-126273, period 12, copy # 18.6 with 100% matches and no inserts/deletes, 2) 126571-126709, period 16, copy # 8.7 with 99% matches and no inserts/deletes and 3) 126810-127142, period 17, copy # 19.6 with 100% matches and no inserts/deletes.]
LTR c	2.00	126371,132413 145820,151862		HHVONE063 , HHVONE060.1 , IGR49, IGR50, HHVONE077 , HHVONE078 , IGR61, IGR62	positive and negative gene regulator, ICP4 (ICP4_HSV11) latency associated transcript, LAT This region contains three tandem nucleotide repeats at genome coordinates 1) 126051-126273, period 12, copy # 18.6 with 100% matches and no inserts/deletes, 2) 126571-126709, period 16, copy # 8.7 with 99% matches and no inserts/deletes and 3) 126810-127142, period 17, copy # 19.6 with 100% matches and no inserts/deletes. This region contains a tandem nucleotide repeat at genome coordinates 132388-132513, period 22, copy # 5.7 with 99% matches and no inserts/deletes. positive and negative gene regulator, ICP4 (ICP4_HSV11) latency associated transcript, 3' segment intergenic region [This region contains one tandem nucleotide repeat at genome coordinates 145676-145845, period 22, copy # 7.7 with 97% matches and no inserts/deletes. ] intergenic region [This region contains three tandem nucleotide repeats at genome coordinates 1) 151091-151423, period 17, copy # 19.6 with 100% matches and no inserts/deletes, 2) 151524-151662, period 16, copy # 8.7 with 99% matches and no inserts/deletes and 3) 151960-152182, period 12, copy # 18.6 with 100% matches and no inserts/deletes. ]