#/mnt/gattaca/jhughes/alignace/all_motifs_3
#0	YBL042C_YBL041W 986 bp YBL042C FUI1 1-1920 uridine permease YBL041W PRE7 1-726 proteasome subunit
#1	YDL020C 500 bp YDL020C RPN4 1-1596 involved in ubiquitin degradation pathway
#2	YDL097C_YDL095W 363 bp YDL097C RPN6 1-1305 Subunit of the regulatory particle of the proteasome YDL095W PMT1 1-2454 dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase
#3	YDL148C_YDL147W 337 bp YDL148C  1-2433  YDL147W RPN5 1-1338 Subunit of the regulatory particle of the proteasome
#4	YDR069C 378 bp YDR069C DOA4 1-2781 ubiquitin isopeptidase
#5	YDR394W 409 bp YDR394W RPT3 1-1287 probable 26S protease subunit and member of the CDC48\/PAS1\/SEC18 family of ATPases
#6	YDR427W 198 bp YDR427W RPN9 1-1182 Subunit of the regulatory particle of the proteasome
#7	YER012W 500 bp YER012W pre1 1-597 22.6 kDa proteasome subunit
#8	YER021W 430 bp YER021W RPN3 1-1572 component of the regulatory module of the 26S proteasome, homologous to human p58 subunit
#9	YER094C_YER095W 633 bp YER094C PUP3 1-618  YER095W rad51 1-1203 RecA homolog\; Rad51p colocalizes to ~65 spots with Dmc1p prior to synapsis (independently of ZIP1 and DMC1), and interacts with Rad52p and Rad55p by two-hybrid analysis\; human Rad51p homolog interacts with Brca2 protein which has been implicated in causing breast cancer
#10	YFR050C 297 bp YFR050C PRE4 1-801 proteasome subunit necessary for peptidyl glutamyl peptide hydrolyzing activity
#11	YFR051C_YFR052W 701 bp YFR051C RET2 1-1641  YFR052W RPN12 1-825 cytoplasmic 32 - 34 kDa protein
#12	YGL011C_YGL010W 297 bp YGL011C SCL1 1-759 Proteasome subunit YC7alpha\/Y8 (protease yscE subunit 7) YGL010W  1-525 
#13	YGL048C_YGL047W 265 bp YGL048C RPT6 1-1218 ATPase YGL047W  1-609 
#14	YGR135W 253 bp YGR135W PRE9 1-777 proteasome component Y13
#15	YGR253C 500 bp YGR253C PUP2 1-783 Proteasome subunit
#16	YHR027C 266 bp YHR027C RPN1 1-2982 Subunit of 26S Proteasome (PA700 subunit)
#17	YHR199C_YHR200W 656 bp YHR199C  1-933  YHR200W RPN10 1-807 homolog of the mammalian S5a protein, component of 26S proteasome
#18	YIL007C_YIL006W 405 bp YIL007C  1-663  YIL006W  1-1122 
#19	YIL075C 380 bp YIL075C RPN2 1-2838 RPN2p is a component of the 26S proteosome
#20	YJL002C_YJL001W 511 bp YJL002C OST1 1-1431 64-kDa, alpha subunit of oligosaccharyltransferase complex\; homologous to mammalian ribophorin I YJL001W PRE3 1-65, 182-764 Subunit of 20S proteasome
#21	YKL145W 351 bp YKL145W RPT1 1-1404 putative ATPase, 26S protease subunit component
#22	YML092C 383 bp YML092C PRE8 1-753 proteasome component Y7
#23	YMR313C_YMR314W 401 bp YMR313C  1-1929  YMR314W PRE5 1-705 alpha-type of subunit of 20S proteasome
#24	YOL038W 500 bp YOL038W PRE6 1-765 alpha-type of subunit of 20S proteasome
#25	YOR116C_YOR117W 883 bp YOR116C RPO31 1-4383 RNA polymerase III large subunit YOR117W RPT5 1-1305 
#26	YOR157C_YOR158W 412 bp YOR157C pup1 1-786 putative proteasome subunit YOR158W pet123 1-957 Mitochondrial ribosomal protein of small subunit
#27	YOR259C_YOR260W 275 bp YOR259C RPT4 1-1314 ATPase\; component of the 26S proteasome cap subunit YOR260W gcd1 1-1737 translation initiation factor eIF2b gamma subunit\; negative regulator in the general control of amino acid biosynthesis
#28	YOR261C_YOR262W 359 bp YOR261C RPN8 1-1017 Subunit of the regulatory particle of the proteasome YOR262W  1-1044 
#29	YOR362C 500 bp YOR362C PRE10 1-867 proteasome component YC1 (protease yscE subunit 1)
#30	YPL074W 400 bp YPL074W  1-2265 
#31	YPR102C_YPR103W 600 bp YPR102C RPL11A 1-525 Ribosomal protein L11A (L16A) (rp39A) (YL22) YPR103W PRE2 1-864 proteasome subunit
#32	YPR107C_YPR108W 389 bp YPR107C YTH1 1-627  YPR108W RPN7 1-1290 Subunit of the regulatory particle of the proteasome

#Motif 1
TTTTGCCACC	0	899	0
ATTTGCCACC	2	103	1
TTTTGCCACC	3	199	0
TTTTGCCACC	5	233	0
TTTTGCCACC	6	89	0
TTTTGCCACC	7	358	0
ATTTGCCACC	8	334	1
TTTTGCCACC	9	173	1
ATTTGCCACC	10	185	1
ATTTGCCACC	11	603	1
ATTTGCCACC	12	99	0
TTTTGCCACC	13	74	1
TTTTGCCACC	14	94	0
TTTTGCCACC	15	396	0
TTTTGCCACC	16	121	0
TTTCGCCACC	17	554	1
TTTTGCCACC	19	261	0
TTTTGCCACC	20	393	0
TTTTGCCACC	21	195	1
TTTTGCCACC	22	263	0
TTTTGCCACT	23	254	0
TTTTGCCACC	24	390	1
TTTTGCTACC	24	431	0
TTTTGCCACC	25	719	0
TTTTGCCACT	26	148	1
ATTTGCCACC	27	103	0
ATTTGCCACT	28	161	1
TTTTGCCACC	29	372	0
TTTTGCCACC	31	445	0
GTTTGCCACC	32	234	1
**********