Stratified Random Picks
                        To make the stratified picks the genome is divided
 into   the   top   20%,   middle  30%, and bottom 50% along two axis - gene
 density   and   nontranscribed     conservation.   Then three random picks
 are taken   from   each strata, and   a  fourth pick in  the strata that
are underrepresented     in the manual picks.      One additional  backup
pick is made in each strata    in case there is an   unforeseen  technical
 problem with a region.  The   backup pick is parenthesized   below.
                   
                   The left coordinate is the June genomic position for the 
 feature     while    
                   the right coordinate is the November genomic position
for   the   feature.
                                            
consNonTx 0% - 50%, gene 0% - 50% (1 manual)
                        June:
          chr13:28500001-29000000    Nov:
          chr13:24500016-25000015  consNonTx  2.8%, gene  0.5%
                        June: 
         chr2:51700001-52200000    Nov: 
         chr2:51837455-52337454   consNonTx  3.8%, gene  0.0%
                        June: 
         chr4:119000001-119500000   Nov: 
         chr4:118527386-119027385   consNonTx  3.9%, gene  0.0%
                        June: 
         chr10:54300001-54800000   Nov: 
         chr10:54489120-54989119   consNonTx  2.8%, gene  1.2%
                        (June: 
         chr5:15900001-16400000    Nov: 
         chr5:16187472-16687471   consNonTx  5.1%, gene  1.7%)
                                               
consNonTx 0% - 50%, gene 50% - 80% (4 manual)
                        June: 
         chr2:115500001-116000000     
         Nov: chr2:116215329-116715328   consNonTx  6.2%, gene  2.3%
                        June: 
         chr18:61100001-61600000    Nov: 
         chr18:61234622-61734621   consNonTx  3.4%, gene  3.4%
                        June: 
         chr12:40500001-41000000    Nov: 
  chr12:40239443-40739442          consNonTx  1.7%, gene  3.1%
                        (June: 
         chr2:196700001-197200000    Nov: 
         chr2:197214044-197714043   consNonTx  5.4%, gene  3.3%)
                                               
consNonTx 0% - 50%, gene 80% - 100% (11 manual)
                        June: 
         chr2:232500001-233000000    Nov: 
         chr2:233173598-233673597   consNonTx  1.3%, gene  4.6%
                        June: 
         chr13:111900001-112400000    Nov: 
         chr13:107927238-108427237   consNonTx  1.1%, gene  5.5%
                        June: 
         chr21:36900001-37400000    Nov: 
         chr21:36983033-37483032   consNonTx  2.3%, gene  5.2%
                        (June: 
         chr4:47800001-48300000    Nov: 
         chr4:48032776-48532775   consNonTx  1.9%, gene  4.4%)
                                               
consNonTx 50% - 80%, gene 0% - 50% (2 manual)
                        June: 
         chr16:25300001-25800000    Nov: 
         chr16:25969826-26469825   consNonTx  9.7%, gene  0.5%
                        June: 
         chr5:141800001-142300000    Nov: 
         chr5:142482586-142982585   consNonTx  6.7%, gene  1.7%
                        June: 
         chr18:25400001-25900000    Nov: 
         chr18:25196197-25696196   consNonTx  7.4%, gene  0.9%
                        (June: 
         chr4:124800001-125300000    Nov: 
         chr4:124166677-124666676   consNonTx  6.3%, gene  0.9%)
                                               
consNonTx 50% - 80%, gene 50% - 80% (4 manual)
                        June: 
         chr5:56000001-56500000    Nov: 
         chr5:57392856-57892855 consNonTx   7.9%, gene  2.2%
                        June: 
         chr6:131800001-132300000    Nov: 
         chr6:132023965-132523964 consNonTx   6.9%, gene  2.1%
                        June: 
         chr6:73700001-74200000    Nov: 
         chr6:73699933-74199932 consNonTx   6.4%, gene  3.6%
                        (June: 
         chr4:53700001-54200000    Nov: 
         chr4:53859184-54359183 consNonTx   9.0%, gene  2.1%)
                                               
consNonTx 50% - 80%, gene 80% - 100% (3 manual)
                        June: 
         chr1:149000001-149500000    Nov: 
         chr1:146905332-147405331  consNonTx 10.2%, gene  8.4%
                        June: 
         chr9:122800001-123300000    Nov: 
         chr9:123331831-123831830  consNonTx  8.3%, gene  5.9%
                        June: 
         chr15:39100001-39600000    Nov: 
        chr15:36628619-37128618 consNonTx  9.7%, gene 10.6%
                        (June: 
         chr17:33400001-33900000    Nov: 
         chr17:35665792-36165791  consNonTx  7.7%, gene  6.1%)
                                               
consNonTx 80% - 100%, gene 0% - 50% (3 manual)
                        June: 
         chr14:51200001-51700000   	Nov: 
        chr14:47673341-48173340 consNonTx 14.9%, gene  0.1%
                        June: 
         chr11:133100001-133600000    Nov: 
         chr11:132612235-133112234  consNonTx 13.5%, gene  0.3%
                        June: 
         chr16:52600001-53100000   Nov: 
         chr16:62362206-62862205  consNonTx 15.4%, gene  0.0%
                        (June: 
         chrX:41900001-42400000    Nov: 
         chrX:42149253-42649252  consNonTx 13.4%, gene  0.7%)
                                               
consNonTx 80% - 100%, gene 50% - 80% (1 manual)
                        June: 
         chr8:117800001-118300000     Nov: 
         chr8:118874200-119374199  consNonTx 11.4%, gene  3.2%
                        June: 
         chr14:96900001-97400000   Nov: 
         chr14:93204045-93704044  consNonTx 15.9%, gene  2.9%
                        June: 
         chrX:117500001-118000000    Nov: 
         chrX:119675382-120175381  consNonTx 10.7%, gene  2.0%
                        June: 
         chr6:108100001-108600000    Nov: 
          chr6:108287568-108787567	consNonTx   18.6%, gene  2.3%
                                               
consNonTx 80% - 100%, gene 80% - 100% (1 manual) 
                        June: 
         chr2:218300001-218800000    Nov: 
         chr2:218998720-219498719  consNonTx 13.3%, gene  9.1%
                        June: 
         chr11:66700001-67200000	   Nov: 
         chr11:65865884-66365883  consNonTx 13.4%, gene  9.0%
                        June: 
         chr20:33600001-34100000    Nov: 
         chr20:33559944-34059943	consNonTx   11.5%, gene  9.2%
                        June: 
         chr6:41300001-41800000	   Nov: 
         chr6:41294331-41794330  consNonTx 15.2%, gene  4.8%
                        (June: 
         chr9:124300001-124800000	   Nov: 
         chr9:124831831-125331830 consNonTx  11.4%, gene  5.4%)
                                                
Stratification of Manual Picks
               Here is the noncoding conservation and gene density of non-overlapping 
         500 kb regions in the manual picks.   The boundaries between strata 
   are:                             
low 50%  middle 30%  high 20%
         ------------------------------
gene      0.0-1.9%  1.9-4.2%   4.2-100%
consNotTx 0.0-6.3%  6.3-10.6% 10.6-100%
CFTR 
June: chr7:114288355-116165780   Nov: chr7:114288155-116165580
  
Interleukin_Cluster 
June: chr5:130778557-131778556   Nov: chr5:131703638-132703637  
   
Apo_Cluster 
June: chr11:118810001-119310000   Nov: chr11:117969240-118469239
   
Chr22 
June: chr22:28500001-30200000   Nov: chr22:28500001-30200000
  
Chr21 
June: chr21:30323762-32019746   Nov: chr21:30406794-32102778
  
ChrX 
June: chrX:147250001-148500000   Nov: chrX:149572309-150846234
  
Chr19 
June: chr19:55200001-56200000   Nov: chr19:54724484-55728861 
   
Alpha_Globin 
June: chr16:79138-579137   Nov: chr16:10001-510000
    
Beta_Globin 
June: chr11:5550000-6549999   Nov: chr11:5076527-6078118
  
HOXA_cluster 
June: chr7:26600001-27100000   Nov: chr7:26599801-27099800
IGF2/H19 
June: chr11:300001-900000   Nov: chr11:1941933-2547980 PROBLEMATIC REGION - SUBSTANTIALLY REARRANGED BETWEEN JUNE AND NOVEMBER BUILDS
FOXP2 
June: chr7:112410791-113410790   Nov: chr7:112410791-113410790
   
                                                
Semi-Manual Picks
                         Here's the stratification of the other zoo-seq regions.
    I  recommend      picking  7q21.13 and 7q31.33 to round things out. 
                         
7q21.13 
June: chr7:88319137-89433560  Nov: chr7:88318937-89433360
  
7q21.3 
June: chr7:91589227-92559635  Nov: chr7:91589027-92559435
 
7q21.3 
June: chr7:93650712-94868826Nov: chr7:93650512-94868626
  
7q31.33 
June: chr7:124556444-125719632   Nov: chr7:124556244-125719432
   
7q32.1 
June: chr7:126427707-127330661   Nov: chr7:126427507-127330461
                                        
         
Methods
                                        
        
Gene density is defined as percentage of bases covered
    either by Ensembl        genes, or human mRNA best blat alignments in
the    UCSC browser database.        
                                        
         
Nontranscribed transcription was measured by a fairly
elaborate process.         125 base non-overlapping subwindows were taken
inside of the 500,000    base    windows.   Subwindows with less than 75%
of their bases in a mouse    alignment    were thrown out.   For the remaining
subwindows the percentage    with at least   80% base identity is used as
the conservation score.  To   get the nontranscribed   conservation score
the mouse alignments in regions   corresponding to Ensembl   genes, all genbank
mRNA blastz alignments, Fgenesh++   gene predictions, twinScan   gene predictions,
 spliced EST alignments, and  repeats  were thrown out.