Distribution of restriction sites in the human genome

Enzyme:  SexAI               Longest uncut segments
Specificity:  ACCWGGT               Repeats in uncut segments
Number of sites:  295100               Genes in uncut segments
Mean distance between sites:  9696 base pairs
Standard deviation:  10446 base pairs
Site density 103.1 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   504475  chr15  NT_037852.6  1397101-1901576    1.13 % in   34 repeats    1.68 % in 1 genes
2   440417  chr6  NT_167244.1  2346538-2786955    4.90 % in   87 repeats    1.45 % in 1 genes
3   314611  chr7  NT_077528.2  1-314612    81.50 % in   94 repeats    0.00 % in 0 genes
4   310317  chrY  NT_011875.12  8405579-8715896    82.02 % in   38 repeats    0.00 % in 0 genes
5   246783  chr19  NT_011109.16  1-246784    99.80 % in   61 repeats    0.00 % in 0 genes
6   233212  chr11  NT_009237.18  48611685-48844897    98.15 % in   53 repeats    0.00 % in 0 genes
7   218654  chr4  NT_006316.16  364125-582779    12.80 % in   131 repeats    18.94 % in 25 genes
8   218207  chr6  NT_167244.1  4388837-4607044    4.19 % in   21 repeats    0.00 % in 0 genes
9   218048  chr12  NT_029419.12  320571-538619    99.74 % in   50 repeats    0.00 % in 0 genes
10   214662  chrX  NT_011630.14  5876714-6091376    99.69 % in   41 repeats    0.00 % in 0 genes
11   205437  chr6  NT_167248.1  509723-715160    14.04 % in   54 repeats    0.00 % in 0 genes
12   193720  chr6  NT_167244.1  3784884-3978604    3.49 % in   30 repeats    0.00 % in 0 genes
13   191561  chr6  NT_167244.1  3169257-3360818    4.26 % in   48 repeats    0.00 % in 0 genes
14   188404  chr5  NW_003315917.1  1143789-1332193    24.71 % in   130 repeats    0.00 % in 0 genes
15   186646  chr6  NT_167247.1  4417383-4604029    2.86 % in   28 repeats    0.00 % in 0 genes
16   180505  chr6  NT_167249.1  2131621-2312126    5.71 % in   45 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 
1  504475  chr15  NT_037852.6  1397101-1901576    34  22       AT_rich (5)  (TA)n (3)  L2a (3) 
2  440417  chr6  NT_167244.1  2346538-2786955    87  48       AluY (7)  AT_rich (4)  AluSx (4) 
3  314611  chr7  NT_077528.2  1-314612    94  26       ALR/Alpha (34)  L1PA2 (8)  AT_rich (8) 
4  310317  chrY  NT_011875.12  8405579-8715896    38  14       LTR12B (17)  L1PA7 (3)  AT_rich (3) 
5  246783  chr19  NT_011109.16  1-246784    61  12       ALR/Alpha (33)  L1PA3 (13)  L1PA4 (3) 
6  233212  chr11  NT_009237.18  48611685-48844897    53  12       ALR/Alpha (28)  L1PA4 (5)  L1PA2 (4) 
7  218654  chr4  NT_006316.16  364125-582779    131  52       (CA)n (48)  AT_rich (8)  L1M4 (7) 
8  218207  chr6  NT_167244.1  4388837-4607044    21  14       HERVH-int (4)  AluSx (3)  MER57-int (2) 
9  218048  chr12  NT_029419.12  320571-538619    50  13       ALR/Alpha (30)  L1PA4 (3)  L1PA3 (3) 
10  214662  chrX  NT_011630.14  5876714-6091376    41  10       ALR/Alpha (27)  L1PA4 (3)  L1PA3 (3) 
11  205437  chr6  NT_167248.1  509723-715160    54  39       AT_rich (7)  L2c (3)  L2b (3) 
12  193720  chr6  NT_167244.1  3784884-3978604    30  22       L2a (5)  MLT1H-int (2)  L1M5 (2) 
13  191561  chr6  NT_167244.1  3169257-3360818    48  23       AluSx (9)  L1MC5 (4)  L1MB3 (4) 
14  188404  chr5  NW_003315917.1  1143789-1332193    130  67       AT_rich (17)  MSTA (5)  (TA)n (4) 
15  186646  chr6  NT_167247.1  4417383-4604029    28  22       AluSx (3)  MLT1J (2)  L1MC5 (2) 
16  180505  chr6  NT_167249.1  2131621-2312126    45  22       Charlie2b (6)  AluSx (6)  L1MB8 (3) 

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Genes in longest uncut segments
Sgmnt   Length (bp)  Chr  Scaffold  Coordinates  Gene symbol  Gene function 
1   504475       chr15  NT_037852.6  1397101-1901576    LOC100418897 
2   440417       chr6  NT_167244.1  2346538-2786955    MICB  MHC_class_I_polypeptide-related_sequence_B_precursor
7   218654       chr4  NT_006316.16  364125-582779    LOC100287144  ubiquitin_carboxyl-terminal_hydrolase_17-like
LOC100287178  ubiquitin_carboxyl-terminal_hydrolase_17-like
LOC100287205  ubiquitin_carboxyl-terminal_hydrolase_17-like
LOC100287238  ubiquitin_carboxyl-terminal_hydrolase_17-like
LOC100287270 
LOC100288520  ubiquitin_carboxyl-terminal_hydrolase_17-like
LOC100287302 
LOC100287327  ubiquitin_carboxyl-terminal_hydrolase_17-like
LOC100287364  ubiquitin_carboxyl-terminal_hydrolase_17-like
LOC100287404  ubiquitin_carboxyl-terminal_hydrolase_17-like
LOC100287441  ubiquitin_carboxyl-terminal_hydrolase_17-like
LOC100287478  ubiquitin_carboxyl-terminal_hydrolase_17-like
LOC100287513  ubiquitin_carboxyl-terminal_hydrolase_17-like
LOC728369  ubiquitin_carboxyl-terminal_hydrolase_17
LOC728373  ubiquitin_carboxyl-terminal_hydrolase_17-like
LOC728379  ubiquitin_carboxyl-terminal_hydrolase_17-like
USP17L5  ubiquitin_specific_peptidase_17-like_5
LOC728393  ubiquitin_carboxyl-terminal_hydrolase_17-like
LOC728400  ubiquitin_carboxyl-terminal_hydrolase_17-like
LOC728405  ubiquitin_carboxyl-terminal_hydrolase_17-like
USP17  ubiquitin_carboxyl-terminal_hydrolase_17
LOC728419  ubiquitin_carboxyl-terminal_hydrolase_17-like
USP17L6P  ubiquitin_specific_peptidase_17-like_6_(pseudogene)
LOC100287791 
LOC728429 


Posfai@neb.com
May 11, 2011