#/mnt/gattaca/jhughes/alignace/all_motifs_3/organization_of_chromosome_structure.ace
#0	YBL003C_YBL002W 699 bp YBL003C HTA2 1-399 Histone H2A (HTA1 and HTA2 code for nearly identical proteins) YBL002W HTB2 1-396 Histone H2B (HTB1 and HTB2 code for nearly identical proteins)
#1	YBR009C_YBR010W 646 bp YBR009C HHF1 1-312 Histone H4 (HHF1 and HHF2 code for identical proteins) YBR010W HHT1 1-411 Histone H3 (HHT1 and HHT2 code for identical proteins)
#2	YBR275C 500 bp YBR275C RIF1 1-5751 RAP1-interacting factor, involved in establishment of repressed chromatin
#3	YCL011C 500 bp YCL011C GBP2 1-1284 Protein with RNA recognition motifs
#4	YCR052W 254 bp YCR052W RSC6 1-1452 a subunit of RSC, a fifteen-protein chromatin remodeling complex and related to the Swi\/snf Complex.
#5	YDL209C_YDL208W 234 bp YDL209C  1-1020  YDL208W NHP2 1-522 HMG-like nuclear protein
#6	YDL220C_YDL219W 223 bp YDL220C cdc13 1-2775 binds to single-stranded TG1-3 telomere G-tails YDL219W  1-65, 137-524 
#7	YDR081C_YDR082W 359 bp YDR081C pdc2 1-2778 Asparagine and serine-rich protein YDR082W STN1 1-1485 
#8	YDR173C_YDR174W 477 bp YDR173C arg82 1-1068  YDR174W  1-741 
#9	YDR224C_YDR225W 817 bp YDR224C HTB1 1-396 Histone H2B (HTB1 and HTB2 code for nearly identical proteins) YDR225W HTA1 1-399 Histone H2A (HTA1 and HTA2 code for nearly identical proteins)
#10	YDR285W 500 bp YDR285W ZIP1 1-2628 
#11	YER161C 281 bp YER161C spt2 1-1002 non-specific DNA binding protein (sin1)
#12	YFR037C_YFR038W 193 bp YFR037C RSC8 1-1674  YFR038W  1-2337 
#13	YGL238W 186 bp YGL238W CSE1 1-2883 
#14	YGR056W 500 bp YGR056W RSC1 1-2787 Member of RSC complex
#15	YGR098C_YGR099W 440 bp YGR098C esp1 1-4893 vacuolar transporter YGR099W TEL2 1-2067 
#16	YGR218W 500 bp YGR218W CRM1 1-3255 omosome region maintenance protein
#17	YGR285C 500 bp YGR285C ZUO1 1-1302 Zuotin, putative Z-DNA binding protein
#18	YIL127C_YIL126W 347 bp YIL127C  1-621  YIL126W STH1 1-4080 helicase related protein, snf2 homolog
#19	YJR060W 500 bp YJR060W cbf1 1-1056 basic helix-loop-helix protein
#20	YKL049C 500 bp YKL049C CSE4 1-414 high similarity to histone H3 and to human centromere protein CENP-A
#21	YKL089W 184 bp YKL089W mif2 1-1650 Centromere protein required for normal chromosome segregation and spindle integrity
#22	YML103C_YML102W 744 bp YML103C NUP188 1-4968 Nucleoporin YML102W CAC2 1-1407 p60 subunit of the yeast omatin Assembly Factor-I (CAF-I)
#23	YMR071C_YMR072W 303 bp YMR071C  1-504  YMR072W ABF2 1-552 HMG-1 homolog, mitochondrial
#24	YMR094W 268 bp YMR094W CTF13 1-1437 58 kd component (Cbf3c) of the multisubunit 'Cbf3' kinetochore protein complex, which binds to the CDE III element of centromeres
#25	YMR168C 193 bp YMR168C CEP3 1-1827 
#26	YMR240C_YMR241W 720 bp YMR240C CUS1 1-1311 U2 snRNP protein YMR241W  1-945 
#27	YNL031C_YNL030W 676 bp YNL031C HHT2 1-411 Histone H3 (HHT1 and HHT2 code for identical proteins) YNL030W HHF2 1-312 Histone H4 (HHF1 and HHF2 code for identical proteins)
#28	YNR010W 304 bp YNR010W CSE2 1-450 Protein required for accurate mitotic chromosome segregation
#29	YOL012C 500 bp YOL012C HTA3 1-405 An evolutionarily conserved member of the histone H2A F\/Z family of histone variants
#30	YOL104C 248 bp YOL104C NDJ1 1-1059 
#31	YOR213C 311 bp YOR213C SAS5 1-747 
#32	YPL127C_YPL126W 605 bp YPL127C HHO1 1-777 histone H1 YPL126W  1-2691 
#33	YPL128C 500 bp YPL128C TBF1 1-1689 TTAGGG repeat binding factor
#34	YPR017C_YPR018W 558 bp YPR017C DSS4 1-432 GDP dissociation factor for Sec4p YPR018W RLF2 1-1821 p90 subunit of yeast omatin Assembly Factor-I (CAF-I)
#35	YPR052C 305 bp YPR052C NHP6A 1-282 11-kDa nonhistone chromosomal protein

#Motif 3
GAGAAATTTTGAGAAC	0	376	0
GCGAAAAAATGAGAAC	9	244	0
GCGAAAAAGTGAGAAC	9	279	1
GCGAAAATGTGAGAAC	1	357	0
GAGAAATTGTGAGAAC	1	391	0
GAGAAATAATGGGAAC	0	315	1
GCGAAAATTTTGGAAC	9	400	0
GCGAAGTTTTCAGAAC	1	294	1
GCGAAGCTCCCAGAAC	27	381	0
GCGAAGTGCTCGGAAC	27	295	1
GAGAAGCGCTCGGAAC	1	259	1
GTGAAACTATTGGCAC	27	270	0
GTGAAAAGTAGAAAAC	22	507	1
GGGAATAACAGAGAAC	34	0	0
GCGAATTTCAGAGAAC	0	291	0
AAGAAAAAAAGAGAAC	28	212	1
GTGAAAGGCAAGAAAC	16	393	1
GTAAAAGGGGAAGAAC	27	26	1
GGAAAAGATAAAGAAC	19	81	1
GAAAAACACAAAGAAC	2	243	0
GCGAAGCGGTGGGCAC	0	347	0
GTGAAAGAAAAGCAAC	4	177	1
ACGAAAATGGTAGCAC	0	247	1
AAGAAAAGTAAAAAAC	5	194	1
ACGAAAACAACAAAAC	29	309	1
AAGAAATTATCAAAAC	7	129	0
* ****     *****