Distribution of restriction sites in the human genome

Enzyme:  StuI               Longest uncut segments
Specificity:  AGGCCT               Repeats in uncut segments
Number of sites:  800355               Genes in uncut segments
Mean distance between sites:  3575 base pairs
Standard deviation:  4249 base pairs
Site density 279.7 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   503839  chr15  NT_037852.6  1381801-1885640    2.62 % in   38 repeats    0.00 % in 0 genes
2   403369  chr6  NT_167244.1  2359950-2763319    0.05 % in   2 repeats    0.00 % in 0 genes
3   246174  chr6  NT_167244.1  2009351-2255525    0.96 % in   11 repeats    1.79 % in 2 genes
4   210833  chr6  NT_167244.1  4388232-4599065    1.37 % in   10 repeats    0.00 % in 0 genes
5   190259  chr6  NT_167248.1  521524-711783    8.39 % in   40 repeats    2.13 % in 3 genes
6   183168  chr6  NT_167244.1  3173954-3357122    2.19 % in   29 repeats    3.94 % in 2 genes
7   181837  chr6  NT_167244.1  3789125-3970962    0.44 % in   6 repeats    0.00 % in 0 genes
8   173601  chr6  NT_167247.1  4422039-4595640    0.77 % in   4 repeats    100.00 % in 1 genes
9   169182  chr6  NT_167249.1  2138450-2307632    2.08 % in   16 repeats    0.00 % in 0 genes
10   165536  chr6  NT_167247.1  1561185-1726721    0.61 % in   3 repeats    0.00 % in 0 genes
11   163868  chr9  NT_008470.19  21688033-21851901    4.22 % in   24 repeats    0.00 % in 0 genes
12   151501  chr6  NT_167244.1  2894514-3046015    2.05 % in   19 repeats    0.00 % in 0 genes
13   124786  chr1  NT_167185.1  19738-144524    11.94 % in   46 repeats    0.00 % in 0 genes
14   124613  chr6  NT_167244.1  587363-711976    7.54 % in   35 repeats    0.00 % in 0 genes
15   123351  chr6  NT_167245.1  2602338-2725689    3.84 % in   11 repeats    0.00 % in 0 genes
16   122421  chr7  NT_007933.15  68169665-68292086    6.56 % in   29 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 
503839  chr15  NT_037852.6  1381801-1885640    38  21       Tigger2 (6)  L1MDa (6)  MIRb (2) 
403369  chr6  NT_167244.1  2359950-2763319    2       L1MEg (1)  AluSp (1) 
246174  chr6  NT_167244.1  2009351-2255525    11  11       MIRb (1)  MIR (1)  MER5A1 (1) 
210833  chr6  NT_167244.1  4388232-4599065    10  8       MER57-int (2)  AluSx (2)  (TTCC)n (1) 
190259  chr6  NT_167248.1  521524-711783    40  26       AT_rich (7)  L2c (3)  L2b (3) 
183168  chr6  NT_167244.1  3173954-3357122    29  17       AluSx (6)  L1MB3 (4)  GC_rich (3) 
181837  chr6  NT_167244.1  3789125-3970962    6       MLT1H-int (1)  MIR (1)  MER52D (1) 
173601  chr6  NT_167247.1  4422039-4595640    4       (TTAAA)n (1)  MER11A (1)  AluSg/x (1) 
169182  chr6  NT_167249.1  2138450-2307632    16  6       Charlie2b (6)  AluSx (4)  L1MB8 (3) 
10  165536  chr6  NT_167247.1  1561185-1726721    3       MIRc (1)  L1MC3 (1)  A-rich (1) 
11  163868  chr9  NT_008470.19  21688033-21851901    24  17       MIRb (2)  MER5B (2)  LTR67B (2) 
12  151501  chr6  NT_167244.1  2894514-3046015    19  9       L1MC5 (6)  L2c (3)  AluY (2) 
13  124786  chr1  NT_167185.1  19738-144524    46  28       L1PB1 (5)  L2a (4)  AluY (3) 
14  124613  chr6  NT_167244.1  587363-711976    35  25       L2c (3)  L2b (3)  L1MA9 (3) 
15  123351  chr6  NT_167245.1  2602338-2725689    11  9       MLT1N2 (2)  L2 (2)  MLT1E2 (1) 
16  122421  chr7  NT_007933.15  68169665-68292086    29  21       AluSx (4)  L1PB1 (3)  L1MB7 (2) 


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Genes in longest uncut segments
Sgmnt   Length (bp)  Chr  Scaffold  Coordinates  Gene symbol  Gene function 
3   246174       chr6  NT_167244.1  2009351-2255525    FLOT1  flotillin-1
DDR1  epithelial_discoidin_domain-containing_receptor_1_isoform_DDR1c
5   190259       chr6  NT_167248.1  521524-711783    OR12D1P 
OR11A1  olfactory_receptor_11A1
OR10C1  olfactory_receptor_10C1
6   183168       chr6  NT_167244.1  3173954-3357122    EHMT2  histone-lysine_N-methyltransferase,_H3_lysine-9_specific_3_isoform_b
TNXB  tenascin-X_isoform_1_precursor
8   173601       chr6  NT_167247.1  4422039-4595640    LOC100507722  hypothetical_protein_LOC100507722



Posfai@neb.com
May 11, 2011