Distribution of restriction sites in the human genome

Enzyme:  HpyNSH57II               Longest uncut segments
Specificity:  TCNNGA               Repeats in uncut segments
Number of sites:  10163384               Genes in uncut segments
Mean distance between sites:  281 base pairs
Standard deviation:  298 base pairs
Site density3552.0 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   486650  chr15  NT_037852.6  1398728-1885378    0.01 % in   1 repeats    0.00 % in 0 genes
2   401402  chr6  NT_167244.1  2359890-2761292    0.02 % in   1 repeats    0.00 % in 0 genes
3   208217  chr6  NT_167244.1  4389675-4597892    0.17 % in   4 repeats    0.00 % in 0 genes
4   180549  chr6  NT_167244.1  3790297-3970846    0.16 % in   2 repeats    0.00 % in 0 genes
5   175981  chr6  NT_167244.1  3179397-3355378    0.12 % in   5 repeats    0.47 % in 1 genes
6   172703  chr6  NT_167247.1  4421962-4594665    0.24 % in   2 repeats    100.00 % in 1 genes
7   164897  chr6  NT_167249.1  2138148-2303045    0.03 % in   1 repeats    0.00 % in 0 genes
8   159862  chr6  NT_167248.1  521372-681234    0.35 % in   2 repeats    0.00 % in 0 genes
9   150459  chr9  NT_008470.19  21693102-21843561    0.11 % in   1 repeats    0.00 % in 0 genes
10   142849  chr6  NT_167244.1  2894645-3037494    0.02 % in   2 repeats    0.00 % in 0 genes
11   118951  chr6  NT_167245.1  2605556-2724507    1.19 % in   4 repeats    0.00 % in 0 genes
12   114711  chr6  NT_167247.1  1177592-1292303    0.06 % in   1 repeats    0.00 % in 0 genes
13   108383  chr6  NT_167245.1  137844-246227    0.44 % in   3 repeats    0.00 % in 0 genes
14   105477  chr6  NT_167244.1  588520-693997    1.03 % in   7 repeats    0.00 % in 0 genes
15   104620  chr6  NT_167244.1  1451564-1556184    0.03 % in   2 repeats    0.00 % in 0 genes
16   104569  chr6  NT_167244.1  1833183-1937752    0.28 % in   3 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 
486650  chr15  NT_037852.6  1398728-1885378    1       AT_rich (1) 
401402  chr6  NT_167244.1  2359890-2761292    1       AluSp (1) 
208217  chr6  NT_167244.1  4389675-4597892    4       (TTCC)n (1)  MER57-int (1)  AluSg/x (1) 
180549  chr6  NT_167244.1  3790297-3970846    2       MLT1H-int (1)  MER52D (1) 
175981  chr6  NT_167244.1  3179397-3355378    3       GC_rich (3)  (CCG)n (1)  AluSp (1) 
172703  chr6  NT_167247.1  4421962-4594665    2       MER11A (1)  AluSc (1) 
164897  chr6  NT_167249.1  2138148-2303045    1       AT_rich (1) 
159862  chr6  NT_167248.1  521372-681234    2       L1PREC2 (1)  HERVH-int (1) 
150459  chr9  NT_008470.19  21693102-21843561    1       L1M5 (1) 
10  142849  chr6  NT_167244.1  2894645-3037494    2       AluY (1)  AluSg1 (1) 
11  118951  chr6  NT_167245.1  2605556-2724507    3       L2 (2)  MLT1E2 (1)  L2a (1) 
12  114711  chr6  NT_167247.1  1177592-1292303    1       ERV3-16A3_I-int (1) 
13  108383  chr6  NT_167245.1  137844-246227    3       MLT1F (1)  MLT1E2 (1)  LTR12C (1) 
14  105477  chr6  NT_167244.1  588520-693997    5       L1MA9 (3)  L1PB1 (1)  L1P5 (1) 
15  104620  chr6  NT_167244.1  1451564-1556184    2       ERV3-16A3_I-int (1)  AluSg1 (1) 
16  104569  chr6  NT_167244.1  1833183-1937752    3       (TATG)n (1)  MIR (1)  AluSx (1) 


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Genes in longest uncut segments
Sgmnt   Length (bp)  Chr  Scaffold  Coordinates  Gene symbol  Gene function 
5   175981       chr6  NT_167244.1  3179397-3355378    EHMT2  histone-lysine_N-methyltransferase,_H3_lysine-9_specific_3_isoform_b
6   172703       chr6  NT_167247.1  4421962-4594665    LOC100507722  hypothetical_protein_LOC100507722



Posfai@neb.com
May 11, 2011