Distribution of restriction sites in the human genome

Enzyme:  McaCI               Longest uncut segments
Specificity:  CCATC               Repeats in uncut segments
Number of sites:  6095221               Genes in uncut segments
Mean distance between sites:  469 base pairs
Standard deviation:  526 base pairs
Site density2130.2 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   402205  chr6  NT_167244.1  2359031-2761236    0.16 % in   3 repeats    0.00 % in 0 genes
2   208806  chr6  NT_167244.1  4389640-4598446    0.42 % in   5 repeats    0.00 % in 0 genes
3   180665  chr6  NT_167244.1  3790216-3970881    0.19 % in   2 repeats    0.00 % in 0 genes
4   175270  chr6  NT_167244.1  3180211-3355481    0.13 % in   3 repeats    0.01 % in 1 genes
5   173386  chr6  NT_167247.1  4422165-4595551    0.75 % in   3 repeats    100.00 % in 1 genes
6   166915  chr6  NT_167247.1  1562672-1729587    0.62 % in   7 repeats    0.17 % in 1 genes
7   165243  chr6  NT_167249.1  2138263-2303506    0.17 % in   3 repeats    0.00 % in 0 genes
8   159745  chr6  NT_167248.1  521616-681361    0.27 % in   2 repeats    0.00 % in 0 genes
9   155927  chr6  NT_167244.1  2008683-2164610    0.29 % in   3 repeats    0.00 % in 0 genes
10   151101  chr9  NT_008470.19  21692751-21843852    0.38 % in   3 repeats    0.00 % in 0 genes
11   143166  chr6  NT_167244.1  2894323-3037489    0.07 % in   2 repeats    0.00 % in 0 genes
12   118643  chr6  NT_167245.1  2605777-2724420    0.94 % in   3 repeats    0.00 % in 0 genes
13   114895  chr6  NT_167247.1  1177656-1292551    0.01 % in   1 repeats    0.00 % in 0 genes
14   113867  chr6  NT_167246.1  3261129-3374996    0.24 % in   2 repeats    0.00 % in 0 genes
15   108669  chr6  NT_167245.1  137692-246361    0.70 % in   3 repeats    0.00 % in 0 genes
16   105496  chr6  NT_167244.1  588098-693594    0.75 % 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 
402205  chr6  NT_167244.1  2359031-2761236    3       L4 (1)  AluSp (1)  AluJb (1) 
208806  chr6  NT_167244.1  4389640-4598446    5       (TTCC)n (1)  MER57-int (1)  AluSx (1) 
180665  chr6  NT_167244.1  3790216-3970881    2       MLT1H-int (1)  MER52D (1) 
175270  chr6  NT_167244.1  3180211-3355481    3       GC_rich (1)  (CCG)n (1)  AluSp (1) 
173386  chr6  NT_167247.1  4422165-4595551    3       MER11A (1)  AluSg/x (1)  AluSc (1) 
166915  chr6  NT_167247.1  1562672-1729587    5       MIR (2)  L1MEe (2)  (GGAA)n (1) 
165243  chr6  NT_167249.1  2138263-2303506    3       L1MB8 (1)  AT_rich (1)  AluSx (1) 
159745  chr6  NT_167248.1  521616-681361    2       L1PREC2 (1)  HERVH-int (1) 
155927  chr6  NT_167244.1  2008683-2164610    3       MIRb (1)  MIR (1)  AluSx (1) 
10  151101  chr9  NT_008470.19  21692751-21843852    3       MIR3 (1)  LTR67B (1)  L1M5 (1) 
11  143166  chr6  NT_167244.1  2894323-3037489    2       AluY (1)  AluSg1 (1) 
12  118643  chr6  NT_167245.1  2605777-2724420    3       MLT1E2 (1)  L2a (1)  L2 (1) 
13  114895  chr6  NT_167247.1  1177656-1292551    1       ERV3-16A3_I-int (1) 
14  113867  chr6  NT_167246.1  3261129-3374996    2       MIRb (1)  AluSx (1) 
15  108669  chr6  NT_167245.1  137692-246361    3       MLT1F (1)  MLT1E2 (1)  LTR12C (1) 
16  105496  chr6  NT_167244.1  588098-693594    4       L1MA9 (2)  L1PB1 (1)  L1ME3D (1) 


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Genes in longest uncut segments
Sgmnt   Length (bp)  Chr  Scaffold  Coordinates  Gene symbol  Gene function 
4   175270       chr6  NT_167244.1  3180211-3355481    EHMT2  histone-lysine_N-methyltransferase,_H3_lysine-9_specific_3_isoform_b
5   173386       chr6  NT_167247.1  4422165-4595551    LOC100507722  hypothetical_protein_LOC100507722
6   166915       chr6  NT_167247.1  1562672-1729587    LOC100421582  tripartite_motif-containing_protein_26



Posfai@neb.com
May 11, 2011