Distribution of restriction sites in the human genome

Enzyme:  NlaIV               Longest uncut segments
Specificity:  GGNNCC               Repeats in uncut segments
Number of sites:  7057864               Genes in uncut segments
Mean distance between sites:  405 base pairs
Standard deviation:  604 base pairs
Site density2466.6 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   487993  chr15  NT_037852.6  1397157-1885150    0.13 % in   4 repeats    0.00 % in 0 genes
2   401820  chr6  NT_167244.1  2359701-2761521    0.07 % in   1 repeats    0.00 % in 0 genes
3   209347  chr6  NT_167244.1  4389651-4598998    0.68 % in   7 repeats    0.00 % in 0 genes
4   182384  chr6  NT_167244.1  3788797-3971181    0.59 % in   7 repeats    0.00 % in 0 genes
5   175368  chr6  NT_167244.1  3180299-3355667    0.18 % in   2 repeats    0.00 % in 0 genes
6   172374  chr6  NT_167247.1  4421943-4594317    0.04 % in   2 repeats    100.00 % in 1 genes
7   167614  chr6  NT_167249.1  2137165-2304779    1.16 % in   10 repeats    0.00 % in 0 genes
8   159500  chr6  NT_167248.1  521772-681272    0.12 % in   2 repeats    0.00 % in 0 genes
9   150528  chr9  NT_008470.19  21692843-21843371    0.28 % in   1 repeats    0.00 % in 0 genes
10   143520  chr6  NT_167244.1  2894289-3037809    0.29 % in   4 repeats    0.00 % in 0 genes
11   118556  chr6  NT_167245.1  2605110-2723666    0.94 % in   1 repeats    0.00 % in 0 genes
12   114757  chr6  NT_167247.1  1177472-1292229    0.17 % in   1 repeats    0.00 % in 0 genes
13   113971  chr6  NT_167246.1  3261229-3375200    0.41 % in   3 repeats    0.00 % in 0 genes
14   108026  chr6  NT_167245.1  138039-246065    0.11 % in   2 repeats    0.00 % in 0 genes
15   107605  chr6  NT_167244.1  588434-696039    2.51 % in   9 repeats    0.00 % in 0 genes
16   105175  chr6  NT_167244.1  3490397-3595572    1.60 % 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 
487993  chr15  NT_037852.6  1397157-1885150    4       MIRc (1)  MIRb (1)  L1M3 (1) 
401820  chr6  NT_167244.1  2359701-2761521    1       AluSp (1) 
209347  chr6  NT_167244.1  4389651-4598998    6       AluSx (2)  (TTCC)n (1)  MER57-int (1) 
182384  chr6  NT_167244.1  3788797-3971181    6       AT_rich (2)  MLT1H-int (1)  MIR (1) 
175368  chr6  NT_167244.1  3180299-3355667    2       Charlie4a (1)  AluSp (1) 
172374  chr6  NT_167247.1  4421943-4594317    2       MER11A (1)  AluSc (1) 
167614  chr6  NT_167249.1  2137165-2304779    10  6       L1MB8 (3)  AluSx (3)  L1MC4a (1) 
159500  chr6  NT_167248.1  521772-681272    2       L1PREC2 (1)  HERVH-int (1) 
150528  chr9  NT_008470.19  21692843-21843371    1       L1M5 (1) 
10  143520  chr6  NT_167244.1  2894289-3037809    4       L1MC5 (1)  AluY (1)  AluSg1 (1) 
11  118556  chr6  NT_167245.1  2605110-2723666    1       L2a (1) 
12  114757  chr6  NT_167247.1  1177472-1292229    1       ERV3-16A3_I-int (1) 
13  113971  chr6  NT_167246.1  3261229-3375200    2       MIRb (2)  AluSx (1) 
14  108026  chr6  NT_167245.1  138039-246065    2       MLT1E2 (1)  LTR12C (1) 
15  107605  chr6  NT_167244.1  588434-696039    7       L1MA9 (3)  THE1D (1)  MLT1N2 (1) 
16  105175  chr6  NT_167244.1  3490397-3595572    5       LTR78B (1)  L2a (1)  L1M2 (1) 


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Genes in longest uncut segments
Sgmnt   Length (bp)  Chr  Scaffold  Coordinates  Gene symbol  Gene function 
6   172374       chr6  NT_167247.1  4421943-4594317    LOC100507722  hypothetical_protein_LOC100507722



Posfai@neb.com
May 11, 2011