Distribution of restriction sites in the human genome

Enzyme:  BstAPI               Longest uncut segments
Specificity:  GCANNNNNTGC               Repeats in uncut segments
Number of sites:  814879               Genes in uncut segments
Mean distance between sites:  3511 base pairs
Standard deviation:  3769 base pairs
Site density 284.8 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   516174  chr15  NT_037852.6  1396184-1912358    1.95 % in   46 repeats    1.93 % in 1 genes
2   403729  chr6  NT_167244.1  2359236-2762965    0.17 % in   3 repeats    0.00 % in 0 genes
3   247146  chr6  NT_167244.1  2009148-2256294    1.28 % in   13 repeats    1.87 % in 2 genes
4   218105  chr6  NT_167244.1  4382048-4600153    2.43 % in   18 repeats    0.73 % in 1 genes
5   183105  chr6  NT_167244.1  3789602-3972707    1.05 % in   11 repeats    0.00 % in 0 genes
6   182437  chr6  NT_167247.1  4413051-4595488    2.13 % in   13 repeats    97.77 % in 1 genes
7   181184  chr6  NT_167247.1  1553348-1734532    5.27 % in   45 repeats    5.30 % in 1 genes
8   176757  chr6  NT_167244.1  3179873-3356630    0.28 % in   6 repeats    0.45 % in 2 genes
9   171655  chr6  NT_167249.1  2132076-2303731    2.82 % in   23 repeats    0.00 % in 0 genes
10   163758  chr6  NT_167248.1  520112-683870    2.72 % in   2 repeats    0.00 % in 0 genes
11   156770  chr9  NT_008470.19  21688300-21845070    2.80 % in   13 repeats    0.00 % in 0 genes
12   145985  chr6  NT_167244.1  2893764-3039749    1.79 % in   16 repeats    0.00 % in 0 genes
13   125667  chr6  NT_167246.1  3255055-3380722    2.47 % in   18 repeats    0.00 % in 0 genes
14   125053  chr14  NT_026437.12  196969-322022    99.29 % in   10 repeats    0.00 % in 0 genes
15   124298  chr6  NT_167245.1  2603151-2727449    4.25 % in   15 repeats    0.00 % in 0 genes
16   121364  chrY  NT_011875.12  8500739-8622103    58.75 % 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 
516174  chr15  NT_037852.6  1396184-1912358    46  29       AT_rich (5)  L2a (4)  (TA)n (3) 
403729  chr6  NT_167244.1  2359236-2762965    3       L4 (1)  L1MEg (1)  AluSp (1) 
247146  chr6  NT_167244.1  2009148-2256294    13  12       MIRb (2)  MIR (1)  MER5A1 (1) 
218105  chr6  NT_167244.1  4382048-4600153    18  13       MER57-int (3)  AluSx (3)  AluY (2) 
183105  chr6  NT_167244.1  3789602-3972707    11  10       MLT1H-int (2)  (TA)n (1)  MLT1H (1) 
182437  chr6  NT_167247.1  4413051-4595488    13  11       L2b (3)  MIRc (1)  MIRb (1) 
181184  chr6  NT_167247.1  1553348-1734532    45  34       L2c (3)  Tigger7 (2)  MSTD (2) 
176757  chr6  NT_167244.1  3179873-3356630    5       GC_rich (2)  Charlie4a (1)  (CCG)n (1) 
171655  chr6  NT_167249.1  2132076-2303731    23  13       AluSx (4)  AluJo (3)  MLT2B1 (2) 
10  163758  chr6  NT_167248.1  520112-683870    2       L1PREC2 (1)  HERVH-int (1) 
11  156770  chr9  NT_008470.19  21688300-21845070    13  10       LTR67B (2)  L2 (2)  L1M4b (2) 
12  145985  chr6  NT_167244.1  2893764-3039749    16  8       L1MC5 (5)  AluSc (3)  AluY (2) 
13  125667  chr6  NT_167246.1  3255055-3380722    18  12       AluSx (4)  L1MC5 (3)  MIRb (2) 
14  125053  chr14  NT_026437.12  196969-322022    10  7       CER (4)  MER94 (1)  L1PA4 (1) 
15  124298  chr6  NT_167245.1  2603151-2727449    15  12       Tigger1 (2)  MLT1N2 (2)  L2 (2) 
16  121364  chrY  NT_011875.12  8500739-8622103    2       LTR12B (4)  LTR12D (1) 


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Genes in longest uncut segments
Sgmnt   Length (bp)  Chr  Scaffold  Coordinates  Gene symbol  Gene function 
1   516174       chr15  NT_037852.6  1396184-1912358    LOC100418897 
3   247146       chr6  NT_167244.1  2009148-2256294    FLOT1  flotillin-1
DDR1  epithelial_discoidin_domain-containing_receptor_1_isoform_DDR1c
4   218105       chr6  NT_167244.1  4382048-4600153    HLA-DPB2  major_histocompatibility_complex,_class_II,_DP_beta_2_(pseudogene)
6   182437       chr6  NT_167247.1  4413051-4595488    LOC100507722  hypothetical_protein_LOC100507722
7   181184       chr6  NT_167247.1  1553348-1734532    LOC100421582  tripartite_motif-containing_protein_26
8   176757       chr6  NT_167244.1  3179873-3356630    EHMT2  histone-lysine_N-methyltransferase,_H3_lysine-9_specific_3_isoform_b
TNXB  tenascin-X_isoform_1_precursor



Posfai@neb.com
May 11, 2011