Distribution of restriction sites in the human genome

Enzyme:  HpyCH4V               Longest uncut segments
Specificity:  TGCA               Repeats in uncut segments
Number of sites:  14288503               Genes in uncut segments
Mean distance between sites:  200 base pairs
Standard deviation:  209 base pairs
Site density4993.6 per megabase               Help

Distribution of closely spaced sites
Distribution of sites within 7 STD distance

 Help
Longest uncut segments
# Length  Chr  Scaffold  Coordinates  Repeat content Gene content
1   487680  chr15  NT_037852.6  1398700-1886380    0.01 % in   1 repeats    0.00 % in 0 genes
2   401517  chr6  NT_167244.1  2359812-2761329    0.04 % in   1 repeats    0.00 % in 0 genes
3   208728  chr6  NT_167244.1  4389979-4598707    0.39 % in   5 repeats    0.00 % in 0 genes
4   180417  chr6  NT_167244.1  3790325-3970742    0.09 % in   2 repeats    0.00 % in 0 genes
5   175234  chr6  NT_167244.1  3180191-3355425    0.11 % in   3 repeats    0.02 % in 1 genes
6   172183  chr6  NT_167247.1  4422157-4594340    0.05 % in   2 repeats    100.00 % in 1 genes
7   159450  chr6  NT_167248.1  521778-681228    0.09 % in   2 repeats    0.00 % in 0 genes
8   155929  chr6  NT_167244.1  2009189-2165118    0.07 % in   1 repeats    0.52 % in 2 genes
9   150186  chr9  NT_008470.19  21693158-21843344    0.07 % in   1 repeats    0.00 % in 0 genes
10   143217  chr6  NT_167244.1  2894511-3037728    0.23 % in   4 repeats    0.00 % in 0 genes
11   117592  chr6  NT_167245.1  2606228-2723820    0.07 % in   2 repeats    0.00 % in 0 genes
12   115755  chr6  NT_167247.1  1177441-1293196    0.19 % in   1 repeats    0.00 % in 0 genes
13   107987  chr6  NT_167245.1  138022-246009    0.08 % in   2 repeats    0.00 % in 0 genes
14   105125  chr6  NT_167244.1  1451484-1556609    0.50 % in   2 repeats    0.00 % in 0 genes
15   104569  chr6  NT_167244.1  588731-693300    0.32 % in   2 repeats    0.00 % in 0 genes
16   104196  chr6  NT_167244.1  1833706-1937902    0.21 % in   1 repeats    0.00 % in 0 genes

Help
Repeats in longest uncut segments
# Length  Chr  Scaffold  Coordinates  Repeats
Total  Distinct    Most  Second  Third 
1  487680  chr15  NT_037852.6  1398700-1886380    1  1       AT_rich (1) 
2  401517  chr6  NT_167244.1  2359812-2761329    1  1       AluSp (1) 
3  208728  chr6  NT_167244.1  4389979-4598707    5  4       AluSx (2)  L1MC (1)  AluSg/x (1) 
4  180417  chr6  NT_167244.1  3790325-3970742    2  2       MLT1H-int (1)  MER52D (1) 
5  175234  chr6  NT_167244.1  3180191-3355425    3  3       GC_rich (1)  (CCG)n (1)  AluSp (1) 
6  172183  chr6  NT_167247.1  4422157-4594340    2  2       MER11A (1)  AluSc (1) 
7  159450  chr6  NT_167248.1  521778-681228    2  2       L1PREC2 (1)  HERVH-int (1) 
8  155929  chr6  NT_167244.1  2009189-2165118    1  1       MIRb (1) 
9  150186  chr9  NT_008470.19  21693158-21843344    1  1       L1M5 (1) 
10  143217  chr6  NT_167244.1  2894511-3037728    4  4       L1MC5 (1)  AluY (1)  AluSg1 (1) 
11  117592  chr6  NT_167245.1  2606228-2723820    2  2       L2a (1)  L2 (1) 
12  115755  chr6  NT_167247.1  1177441-1293196    1  1       ERV3-16A3_I-int (1) 
13  107987  chr6  NT_167245.1  138022-246009    2  2       MLT1E2 (1)  LTR12C (1) 
14  105125  chr6  NT_167244.1  1451484-1556609    2  2       ERV3-16A3_I-int (1)  AluSg1 (1) 
15  104569  chr6  NT_167244.1  588731-693300    2  2       L1PB1 (1)  L1MA9 (1) 
16  104196  chr6  NT_167244.1  1833706-1937902    1  1       AluSx (1) 

Help
Genes in longest uncut segments
Sgmnt   Length (bp)  Chr  Scaffold  Coordinates  Gene symbol  Gene function 
5   175234       chr6  NT_167244.1  3180191-3355425    EHMT2  histone-lysine_N-methyltransferase,_H3_lysine-9_specific_3_isoform_b
6   172183       chr6  NT_167247.1  4422157-4594340    LOC100507722  hypothetical_protein_LOC100507722
8   155929       chr6  NT_167244.1  2009189-2165118    FLOT1  flotillin-1
DDR1  epithelial_discoidin_domain-containing_receptor_1_isoform_DDR1c


Posfai@neb.com
May 11, 2011