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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 | Repeat Type | Copy # | Location | Length | Gene & Intergenic Id(s) | Definitions-Comments |
| tan1 | tandem | 18.60 | 98,320 | HHVONE000 , IGR1 | latency associated transcript, 5' segment intergenic region [This region contains one tandem nucleotide repeat with genomic coordinates 98-320, period 12, copy # 18.6, with 100% matches and no inserts/deletes.] |
|
| tan2 | tandem | 5.90 | 988,1040 | HHVONE001 , HHVONE001.1 , HHVONE001.2 , HHVONE000 | anti-host defense factor, ICP34.5 unknown unknown latency associated transcript, 5' segment |
|
| tan3 | tandem | 3.20 | 2341,2388 | HHVONE002 , HHVONE000 | promiscuous transactivator, cellular homolog, ICP0, VMW110, IE110 (ICP0_HSV11) latency associated transcript, 5' segment |
|
| tan4 | tandem | 2.20 | 2453,2482 | HHVONE002 , HHVONE000 | promiscuous transactivator, cellular homolog, ICP0, VMW110, IE110 (ICP0_HSV11) latency associated transcript, 5' segment |
|
| tan5 | tandem | 2.40 | 2465,2590 | HHVONE002 , HHVONE000 | promiscuous transactivator, cellular homolog, ICP0, VMW110, IE110 (ICP0_HSV11) latency associated transcript, 5' segment |
|
| tan6 | tandem | 4.20 | 4137,4161 | HHVONE002 , HHVONE000 | promiscuous transactivator, cellular homolog, ICP0, VMW110, IE110 (ICP0_HSV11) latency associated transcript, 5' segment |
|
| tan7 | tandem | 9.50 | 5726,5877 | HHVONE000 , IGR2 | latency associated transcript, 5' segment intergenic region [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. ] |
|
| tan8 | tandem | 2.90 | 7903,7928 | IGR2 | intergenic region [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. ] | |
| tan9 | tandem | 6.40 | 8552,8583 | IGR2 | intergenic region [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. ] | |
| tan10 | tandem | 10.60 | 9032,9212 | IGR2 | intergenic region [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. ] | |
| tan11 | tandem | 2.20 | 30195,30220 | HHVONE017 , HHVONE018 | DNA cleavage/packaging protein (VTER_HSV11) virion protein (UL16_HSV11) |
|
| tan12 | tandem | 35.00 | 71605,71814 | HHVONE039 | very large tegument protein, ICP1/2 (TEGU_HSV11) | |
| tan13 | tandem | 3.10 | 79393,79439 | HHVONE039 | very large tegument protein, ICP1/2 (TEGU_HSV11) | |
| tan14 | tandem | 10.76 | 117158,117340 | IGR47 | 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.] | |
| tan15 | tandem | 6.40 | 117788,117819 | IGR47 | 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.] | |
| tan16 | tandem | 2.90 | 118443,118468 | IGR47 | 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.] | |
| tan17 | tandem | 9.40 | 120494,120645 | HHVONE060.1 , IGR47 | 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.] |
|
| tan18 | tandem | 4.20 | 122210,122234 | HHVONE061 , HHVONE060.1 | promiscuous transactivator, cellular homolog, ICP0, VMW110, IE110 (ICP0_HSV11) latency associated transcript, LAT |
|
| tan19 | tandem | 2.40 | 123780,123906 | HHVONE061 , HHVONE060.1 | promiscuous transactivator, cellular homolog, ICP0, VMW110, IE110 (ICP0_HSV11) latency associated transcript, LAT |
|
| tan20 | tandem | 2.20 | 123889,123918 | HHVONE061 , HHVONE060.1 | promiscuous transactivator, cellular homolog, ICP0, VMW110, IE110 (ICP0_HSV11) latency associated transcript, LAT |
|
| tan21 | tandem | 2.40 | 123903,123999 | HHVONE061 , HHVONE060.1 | promiscuous transactivator, cellular homolog, ICP0, VMW110, IE110 (ICP0_HSV11) latency associated transcript, LAT |
|
| tan22 | tandem | 4.10 | 123983,124043 | HHVONE061 , HHVONE060.1 | promiscuous transactivator, cellular homolog, ICP0, VMW110, IE110 (ICP0_HSV11) latency associated transcript, LAT |
|
| tan23 | tandem | 5.90 | 125331,125383 | HHVONE062 , HHVONE061.1 , HHVONE061.2 , HHVONE060.1 | anti-host defense factor, ICP34.5 unknown unknown latency associated transcript, LAT |
|
| tan24 | tandem | 18.60 | 126051,126273 | HHVONE060.1 , IGR49 | latency associated transcript, LAT 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.] |
|
| tan25 | tandem | 8.70 | 126571,126709 | HHVONE060.1 , IGR49 | latency associated transcript, LAT 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.] |
|
| tan26 | tandem | 19.60 | 126810,127142 | HHVONE060.1 , IGR49 | latency associated transcript, LAT 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.] |
|
| tan27 | tandem | 2.20 | 130976,131001 | HHVONE063 | positive and negative gene regulator, ICP4 (ICP4_HSV11) | |
| tan28 | tandem | 5.70 | 132388,132513 | IGR50 | intergenic region [This region contains a tandem nucleotide repeat at genome coordinates 132388-132513, period 22, copy # 5.7 with 99% matches and no inserts/deletes.] | |
| tan29 | tandem | 1.90 | 132760,132816 | HHVONE064 | transcription factor, ICP22 (IE68_HSV11) | |
| tan30 | tandem | 3.10 | 140404,140469 | HHVONE070 | glycoprotein I, gI (VGLI_HSV11) | |
| tan31 | tandem | 10.20 | 143712,143864 | IGR59 | intergenic region [This region contains two tandem nucleotide repeats superimposed at genome coordinates 143712-143858, period 4, copy # 39.0 with 76% matches and 17 inserts/deletes and 143712-143864, period 15, copy # 10.2 with 100% matches and no inserts/deletes.] | |
| tan32 | tandem | 3.30 | 144809,144868 | HHVONE074 , HHVONE075 | tegument protein (US10_HSV11) RNA-binding tegument protein (DNB_HSV11) |
|
| tan33 | tandem | 7.70 | 145676,145845 | IGR61 | 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. ] | |
| tan34 | tandem | 2.20 | 147232,147257 | HHVONE077 | positive and negative gene regulator, ICP4 (ICP4_HSV11) | |
| tan35 | tandem | 19.60 | 151091,151423 | HHVONE078 , IGR62 | 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. ] |
|
| tan36 | tandem | 8.70 | 151524,151662 | HHVONE078 , IGR62 | 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. ] |
|
| tan37 | tandem | 18.60 | 151960,152182 | HHVONE078 , IGR62 | 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 a | inverted | 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 | inverted | 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 | inverted | 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. ] |
|
| LTR | terminal | 1.00 | 1,8786 117585,132413 145820,152261 |
HHVONE001 , HHVONE002 , HHVONE001.1 , HHVONE001.2 , HHVONE000 , IGR1, IGR2, IGR1.1, HHVONE061 , HHVONE062 , HHVONE063 , HHVONE061.1 , HHVONE061.2 , HHVONE060.1 , IGR47, IGR48, IGR49, IGR50, HHVONE077 , HHVONE078 , IGR61, IGR62 | 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 positive and negative gene regulator, ICP4 (ICP4_HSV11) unknown unknown latency associated transcript, LAT 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. 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. ] |