Distribution of restriction sites in the human genome

Enzyme:  R2.BspD6I               Longest uncut segments
Specificity:  GACTC               Repeats in uncut segments
Number of sites:  3888437               Genes in uncut segments
Mean distance between sites:  735 base pairs
Standard deviation:  799 base pairs
Site density1359.0 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   488162  chr15  NT_037852.6  1398493-1886655    0.01 % in   1 repeats    0.00 % in 0 genes
2   402693  chr6  NT_167244.1  2359682-2762375    0.07 % in   1 repeats    0.00 % in 0 genes
3   208209  chr6  NT_167244.1  4389943-4598152    0.16 % in   2 repeats    0.00 % in 0 genes
4   182295  chr6  NT_167244.1  3788401-3970696    0.51 % in   7 repeats    0.00 % in 0 genes
5   176457  chr6  NT_167244.1  3179298-3355755    0.26 % in   6 repeats    0.53 % in 1 genes
6   173951  chr6  NT_167247.1  4421596-4595547    0.74 % in   3 repeats    100.00 % in 1 genes
7   167925  chr6  NT_167247.1  1562677-1730602    1.02 % in   8 repeats    0.16 % in 1 genes
8   165270  chr6  NT_167249.1  2137979-2303249    0.04 % in   2 repeats    0.00 % in 0 genes
9   159991  chr6  NT_167248.1  521689-681680    0.43 % in   2 repeats    0.00 % in 0 genes
10   150482  chr9  NT_008470.19  21693188-21843670    0.08 % in   2 repeats    0.00 % in 0 genes
11   144496  chr6  NT_167244.1  2894227-3038723    0.89 % in   9 repeats    0.00 % in 0 genes
12   118096  chr6  NT_167245.1  2605537-2723633    0.59 % in   1 repeats    0.00 % in 0 genes
13   115141  chr6  NT_167247.1  1177494-1292635    0.15 % in   1 repeats    0.00 % in 0 genes
14   114456  chr6  NT_167246.1  3260664-3375120    0.35 % in   3 repeats    0.00 % in 0 genes
15   108736  chr6  NT_167245.1  137582-246318    0.77 % in   3 repeats    0.00 % in 0 genes
16   107417  chr6  NT_167244.1  588366-695783    2.35 % in   8 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 
488162  chr15  NT_037852.6  1398493-1886655    1       AT_rich (1) 
402693  chr6  NT_167244.1  2359682-2762375    1       AluSp (1) 
208209  chr6  NT_167244.1  4389943-4598152    2       AluSg/x (1)  AluJo (1) 
182295  chr6  NT_167244.1  3788401-3970696    6       AT_rich (2)  MLT1H-int (1)  MIR (1) 
176457  chr6  NT_167244.1  3179298-3355755    4       GC_rich (3)  Charlie4a (1)  (CCG)n (1) 
173951  chr6  NT_167247.1  4421596-4595547    3       MER11A (1)  AluSg/x (1)  AluSc (1) 
167925  chr6  NT_167247.1  1562677-1730602    6       MIR (2)  L1MEe (2)  (GGAA)n (1) 
165270  chr6  NT_167249.1  2137979-2303249    2       L1MC4a (1)  AT_rich (1) 
159991  chr6  NT_167248.1  521689-681680    2       L1PREC2 (1)  HERVH-int (1) 
10  150482  chr9  NT_008470.19  21693188-21843670    2       MIR3 (1)  L1M5 (1) 
11  144496  chr6  NT_167244.1  2894227-3038723    6       L1MC5 (2)  AluSc (2)  AluJo (2) 
12  118096  chr6  NT_167245.1  2605537-2723633    1       L2a (1) 
13  115141  chr6  NT_167247.1  1177494-1292635    1       ERV3-16A3_I-int (1) 
14  114456  chr6  NT_167246.1  3260664-3375120    2       MIRb (2)  AluSx (1) 
15  108736  chr6  NT_167245.1  137582-246318    3       MLT1F (1)  MLT1E2 (1)  LTR12C (1) 
16  107417  chr6  NT_167244.1  588366-695783    6       L1MA9 (3)  MLT1N2 (1)  L1PB1 (1) 


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Genes in longest uncut segments
Sgmnt   Length (bp)  Chr  Scaffold  Coordinates  Gene symbol  Gene function 
5   176457       chr6  NT_167244.1  3179298-3355755    EHMT2  histone-lysine_N-methyltransferase,_H3_lysine-9_specific_3_isoform_b
6   173951       chr6  NT_167247.1  4421596-4595547    LOC100507722  hypothetical_protein_LOC100507722
7   167925       chr6  NT_167247.1  1562677-1730602    LOC100421582  tripartite_motif-containing_protein_26



Posfai@neb.com
May 11, 2011