Distribution of restriction sites in the human genome

Enzyme:  NgoBVIII               Longest uncut segments
Specificity:  GGTGA               Repeats in uncut segments
Number of sites:  5895498               Genes in uncut segments
Mean distance between sites:  485 base pairs
Standard deviation:  530 base pairs
Site density2060.4 per megabase               Help

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

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Longest uncut segments
# Length  Chr  Scaffold  Coordinates  Repeat content Gene content
1   487503  chr15  NT_037852.6  1398787-1886290    0.01 % in   1 repeats    0.00 % in 0 genes
2   401641  chr6  NT_167244.1  2359737-2761378    0.06 % in   1 repeats    0.00 % in 0 genes
3   209011  chr6  NT_167244.1  4390020-4599031    0.53 % in   6 repeats    0.00 % in 0 genes
4   180754  chr6  NT_167244.1  3790288-3971042    0.25 % in   3 repeats    0.00 % in 0 genes
5   176146  chr6  NT_167244.1  3179456-3355602    0.25 % in   6 repeats    0.44 % in 1 genes
6   172667  chr6  NT_167247.1  4422064-4594731    0.28 % in   2 repeats    100.00 % in 1 genes
7   165307  chr6  NT_167249.1  2137796-2303103    0.15 % in   2 repeats    0.00 % in 0 genes
8   164491  chr6  NT_167247.1  1562916-1727407    0.12 % in   2 repeats    0.02 % in 1 genes
9   160378  chr6  NT_167248.1  521172-681550    0.67 % in   2 repeats    0.00 % in 0 genes
10   150921  chr9  NT_008470.19  21692550-21843471    0.44 % in   2 repeats    0.00 % in 0 genes
11   143072  chr6  NT_167244.1  2894494-3037566    0.12 % in   2 repeats    0.00 % in 0 genes
12   118363  chr6  NT_167245.1  2606081-2724444    0.70 % in   4 repeats    0.00 % in 0 genes
13   114832  chr6  NT_167247.1  1177458-1292290    0.18 % in   1 repeats    0.00 % in 0 genes
14   114157  chr6  NT_167246.1  3261257-3375414    0.41 % in   3 repeats    0.00 % in 0 genes
15   108685  chr6  NT_167245.1  137603-246288    0.72 % in   3 repeats    0.00 % in 0 genes
16   105850  chr6  NT_167244.1  587511-693361    0.82 % in   5 repeats    0.00 % in 0 genes

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Repeats in longest uncut segments
# Length  Chr  Scaffold  Coordinates  Repeats
Total  Distinct    Most  Second  Third 
1  487503  chr15  NT_037852.6  1398787-1886290    1  1       AT_rich (1) 
2  401641  chr6  NT_167244.1  2359737-2761378    1  1       AluSp (1) 
3  209011  chr6  NT_167244.1  4390020-4599031    6  5       AluSx (2)  L1ME3D (1)  L1MC (1) 
4  180754  chr6  NT_167244.1  3790288-3971042    3  3       MLT1H-int (1)  MER52D (1)  AluSc (1) 
5  176146  chr6  NT_167244.1  3179456-3355602    6  4       GC_rich (3)  Charlie4a (1)  (CCG)n (1) 
6  172667  chr6  NT_167247.1  4422064-4594731    2  2       MER11A (1)  AluSc (1) 
7  165307  chr6  NT_167249.1  2137796-2303103    2  2       L1MC4a (1)  AT_rich (1) 
8  164491  chr6  NT_167247.1  1562916-1727407    2  2       MIR (1)  AluSq (1) 
9  160378  chr6  NT_167248.1  521172-681550    2  2       L1PREC2 (1)  HERVH-int (1) 
10  150921  chr9  NT_008470.19  21692550-21843471    2  2       LTR67B (1)  L1M5 (1) 
11  143072  chr6  NT_167244.1  2894494-3037566    2  2       AluY (1)  AluSg1 (1) 
12  118363  chr6  NT_167245.1  2606081-2724444    4  3       L2 (2)  MLT1E2 (1)  L2a (1) 
13  114832  chr6  NT_167247.1  1177458-1292290    1  1       ERV3-16A3_I-int (1) 
14  114157  chr6  NT_167246.1  3261257-3375414    3  2       MIRb (2)  AluSx (1) 
15  108685  chr6  NT_167245.1  137603-246288    3  3       MLT1F (1)  MLT1E2 (1)  LTR12C (1) 
16  105850  chr6  NT_167244.1  587511-693361    5  5       MER77 (1)  L1PB1 (1)  L1ME3D (1) 

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Genes in longest uncut segments
Sgmnt   Length (bp)  Chr  Scaffold  Coordinates  Gene symbol  Gene function 
5   176146       chr6  NT_167244.1  3179456-3355602    EHMT2  histone-lysine_N-methyltransferase,_H3_lysine-9_specific_3_isoform_b
6   172667       chr6  NT_167247.1  4422064-4594731    LOC100507722  hypothetical_protein_LOC100507722
8   164491       chr6  NT_167247.1  1562916-1727407    LOC100421582  tripartite_motif-containing_protein_26


Posfai@neb.com
May 11, 2011