(setq glyc-genes '(#$hominis.chro.80198 #$hominis.chro.80199 #$hominis.chro.70063 #$hominis.chro.70062 #$hominis.chro.60434 #$hominis.chro.10337 #$hominis.chro.60435 #$hominis.chro.20231 #$hominis.chro.30172 #$hominis.chro.10234 #$hominis.chro.70113 #$hominis.chro.70488 #$hominis.chro.70351 #$hominis.chro.10335 #$hominis.chro.50184 #$hominis.chro.10337 #$hominis.chro.20336 #$hominis.chro.10196 #$hominis.chro.70471 #$hominis.chro.20343 #$hominis.chro.10418 ))
:: (#$hominis.Chro.80198 #$hominis.Chro.80199 #$hominis.Chro.70063
 #$hominis.Chro.70062 #$hominis.Chro.60434 #$hominis.Chro.10337
 #$hominis.Chro.60435 #$hominis.Chro.20231 #$hominis.Chro.30172
 #$hominis.Chro.10234 #$hominis.Chro.70113 #$hominis.Chro.70488
 #$hominis.Chro.70351 #$hominis.Chro.10335 #$hominis.Chro.50184
 #$hominis.Chro.10337 #$hominis.Chro.20336 #$hominis.Chro.10196
 #$hominis.Chro.70471 #$hominis.Chro.20343 #$hominis.Chro.10418)


(FOR-EACH i in atc-genes
      DO (DISPLAY i *tab* (#^Direction i) *tab*)
      DO (DISPLAY (cadr (cdaadr (SEQUENCE-SIMILAR-TO "TATA" IN (SEQUENCE-OF i FROM -30 TO 1) MISMATCHES 0)))) 
      
      DO (DISPLAY #\Newline))
            )



(FOR-EACH i in glyc-genes
      DO (DISPLAY i *tab* (#^Direction i) *tab*)
      DO (DISPLAY (SPLIT (SEQUENCE-SIMILAR-TO "TATA" IN (SEQUENCE-OF i FROM -30 TO 1) MISMATCHES 0))) 
      
      DO (DISPLAY #\Newline))
            )


;this one works!
(FOR-EACH i in fruc-genes
  WITH a = -80
  WITH b = 1     
  DO (DISPLAY i *tab* (#^Direction i) *tab*)
      DO (DISPLAY (+ a (cadr (cdaadr (SEQUENCE-SIMILAR-TO "TATA" IN (SEQUENCE-OF i FROM a TO b) MISMATCHES 0))))) 
      
      DO (DISPLAY #\Newline))
            )

(FOR-EACH i in fruc-genes
  WITH a = -80
  WITH b = 1     
  DO (DISPLAY i *tab* (#^Direction i) *tab*)
      DO (setf position (THIRD (FIRST (SECOND (SEQUENCE-SIMILAR-TO "TATA" IN (SEQUENCE-OF i FROM a TO b) MISMATCHES 0))))) 
      IF (NUMBERP position) DO (DISPLAY (+ a position) #\Newline) DO (DISPLAY #\Newline)
                   
                        
           )
******************************            
(FOR-EACH metgene in fruc-genes
     WITH left-bound = -80
     WITH right-bound = 1    
     AS direction = (GET-ELEMENT direction FROM metgene)
     AS seq = (SEQUENCE-OF metgene FROM left-bound TO right-bound)
     AS tata-hits = (SECOND (SEQUENCE-SIMILAR-TO "TATA" IN seq MISMATCHES 0))
     DO (DISPLAY-LINE metgene *tab* direction)
        (FOR-EACH hit IN tata-hits
             AS direction = (SECOND hit)
             AS start = (THIRD hit)
             DO (DISPLAY-LINE *tab* (+ a start) *tab* direction *tab* (sequence-of metgene FROM left-bound TO right-bound))))
*******************************

<4>> glyc-genes
:: (#$hominis.Chro.80198 #$hominis.Chro.80199 #$hominis.Chro.70063 #$hominis.Chro.70062 #$hominis.Chro.60434 #$hominis.Chro.10337 #$hominis.Chro.60435 #$hominis.Chro.20231 #$hominis.Chro.30172 #$hominis.Chro.10234 #$hominis.Chro.70113 #$hominis.Chro.70488 #$hominis.Chro.70351 #$hominis.Chro.10335 #$hominis.Chro.50184 #$hominis.Chro.10337 #$hominis.Chro.20336 #$hominis.Chro.10196 #$hominis.Chro.70471 #$hominis.Chro.20343 #$hominis.Chro.10418)
<6>>tca-genes
:: (#$hominis.Chro.70063 #$hominis.Chro.70062 #$hominis.Chro.70433)
<7>> pent-genes
:: (#$hominis.Chro.20231 #$hominis.Chro.30172 #$hominis.Chro.10335
 #$hominis.Chro.20336 #$hominis.Chro.20343)
<8>> ino-genes
:: (#$hominis.Chro.10337)
<9>> pent-genes
:: (#$hominis.Chro.20231 #$hominis.Chro.30172 #$hominis.Chro.10335
 #$hominis.Chro.20336 #$hominis.Chro.20343)
<10>> fruc-genes
:: (#$hominis.Chro.60435 #$hominis.Chro.50115 #$hominis.Chro.20231
 #$hominis.Chro.30172 #$hominis.Chro.20231 #$hominis.Chro.30172
 #$hominis.Chro.20192 #$hominis.Chro.10335 #$hominis.Chro.10337
 #$hominis.Chro.20165 #$hominis.Chro.80224 #$hominis.Chro.40115)

met-genes-52 galac-genes

#$hominis.Chro.60435 #$hominis.Chro.20231 #$hominis.Chro.30172 #$hominis.Chro.30190 #$hominis.Chro.40292 #$hominis.Chro.20343	

met-genes-61 fatty1-genes

#$hominis.Chro.30048 #$hominis.Chro.40326 #$hominis.Chro.30258 #$hominis.Chro.80424 #$hominis.Chro.80425	

met-genes-62 fatty2-genes

#$hominis.Chro.30048

met-genes-71 fatty-meta-genes

#$hominis.Chro.80199 #$hominis.Chro.80198 #$hominis.Chro.30048 #$hominis.Chro.21001 #$hominis.Chro.31000 #$hominis.Chro.41000 #$hominis.Chro.50052 #$hominis.Chro.30084

met-genes-72 ket-genes

NOT FOUND!!!

met-genes-100 ster-genes

#$hominis.Chro.40285 #$hominis.Chro.40285 #$hominis.Chro.10227

met-genes-130 ubiq-genes

#$hominis.Chro.70218 #$hominis.Chro.20298

met-genes-190 ox-phos-genes
;#$hominis.Chro.70559
#$hominis.Chro.50031 #$hominis.Chro.70218 #$hominis.Chro.70218 #$hominis.Chro.70168 #$hominis.Chro.60082 #$hominis.Chro.20424 #$hominis.Chro.80551 #$hominis.Chro.50340 #$hominis.Chro.50039 #$hominis.Chro.10063 #$hominis.Chro.10062 #$hominis.Chro.50302 #$hominis.Chro.80195 #$hominis.Chro.80048 #$hominis.Chro.40070	#$hominis.Chro.20149 #$hominis.Chro.20148 #$hominis.Chro.20424 #$hominis.Chro.50302 #$hominis.Chro.80195 #$hominis.Chro.80048 #$hominis.Chro.40070	#$hominis.Chro.20149 #$hominis.Chro.20148

met-genes-220 urea-amino-genes

#$hominis.Chro.70551 #$hominis.Chro.60426 #$hominis.Chro.70551 #$hominis.Chro.20246

met-genes-230 pur-genes
;#$hominis.Chro.60012 #$hominis.Chro.60090   #$hominis.Chro.60506  #$hominis.Chro.60497 #$hominis.Chro.50255

#$hominis.Chro.60091 #$hominis.Chro.20322 #$hominis.Chro.10234 #$hominis.Chro.50037 #$hominis.Chro.40275 #$hominis.Chro.50237	#$hominis.Chro.40219 #$hominis.Chro.70250 #$hominis.Chro.80373 #$hominis.Chro.40171 #$hominis.Chro.40170 #$hominis.Chro.80027 #$hominis.Chro.50317 #$hominis.Chro.50318	#$hominis.Chro.60382 #$hominis.Chro.10257 #$hominis.Chro.30301 #$hominis.Chro.10225 #$hominis.Chro.80042 #$hominis.Chro.70529 #$hominis.Chro.60525 #$hominis.Chro.20109	#$hominis.Chro.10306 #$hominis.Chro.10312 #$hominis.Chro.30221 #$hominis.Chro.40171 #$hominis.Chro.40170 #$hominis.Chro.70084 #$hominis.Chro.20265	#$hominis.Chro.30484 #$hominis.Chro.80106 #$hominis.Chro.80190 #$hominis.Chro.20334 #$hominis.Chro.20333 #$hominis.Chro.20448 #$hominis.Chro.50026 #$hominis.Chro.30269	#$hominis.Chro.60462 #$hominis.Chro.40214 #$hominis.Chro.40472 #$hominis.Chro.70499 #$hominis.Chro.60194 #$hominis.Chro.60194 	#$hominis.Chro.40352 #$hominis.Chro.30141 #$hominis.Chro.30329 #$hominis.Chro.40352 #$hominis.Chro.50499