#/mnt/gattaca/jhughes/alignace/all_motifs_3/dna_synthesis_and_replication.ace
#0	YAL040C 500 bp YAL040C cln3 1-1743 G(sub)1 cyclin
#1	YAR007C_YAR008W 345 bp YAR007C RFA1 1-1866 69 kDa subunit of the heterotrimeric RPA (RF-A) single-stranded DNA binding protein, binds URS1 and CAR1 YAR008W SEN34 1-828 34kDa subunit of the tetrameric tRNA splicing endonuclease
#2	YBL023C 347 bp YBL023C mcm2 1-2607 
#3	YBL035C 237 bp YBL035C POL12 1-2118 B subunit of DNA polymerase alpha-primase complex
#4	YBR060C 500 bp YBR060C RRR1 1-1863 origin recognition complex subunit 2
#5	YBR086C_YBR087W 723 bp YBR086C  1-2841  YBR087W RFC5 1-1065 Subunit 5 of Replication Factor C\; homologous to human RFC 38 kDa subunit
#6	YBR088C 423 bp YBR088C pol30 1-777 profilerating cell nuclear antigen (PCNA)\; accessory factor for DNA polymerase delta, mRNA increases in G1, peaks in S in mitosis, and increases prior to DNA synthesis in meiosis
#7	YBR160W 349 bp YBR160W cdc28 1-897 protein kinase catalytic subunit
#8	YBR195C 353 bp YBR195C msi1 1-1269 p50 subunit of the yeast omatin Assembly Factor-I (CAF-I) negative regulator of ras-mediated cAMP induction\; homologous to beta subunit of GTP-binding proteins
#9	YBR202W 500 bp YBR202W CDC47 1-2538 Essential for initiation of DNA replication
#10	YBR276C_YBR278W 250 bp YBR276C PPS1 1-2424 dual specificity protein phosphatase YBR278W DPB3 1-606 C and C' subunits of DNA polymerase II
#11	YDL018C_YDL017W 698 bp YDL018C  1-678  YDL017W cdc7 1-1524 serine\/threonine protein kinase
#12	YDL103C_YDL102W 290 bp YDL103C QRI1 1-1434  YDL102W cdc2 1-3294 largest and catalytic subunit of DNA polymerase III (delta)
#13	YDR052C 500 bp YDR052C DBF4 1-2115 cyclin-like kinase required for late nuclear division
#14	YDR054C 500 bp YDR054C cdc34 1-888 ubiquitin-conjugating enzyme, E2
#15	YDR067C_YDR068W 247 bp YDR067C  1-675  YDR068W DOS2 1-933 
#16	YDR109C_YDR110W 434 bp YDR109C  1-2148  YDR110W FOB1 1-1701 DNA replication fork blocking protein
#17	YDR206W 500 bp YDR206W  1-2655 
#18	YDR364C 286 bp YDR364C cdc40 1-1368 Member of the beta transducin family
#19	YEL032W 251 bp YEL032W mcm3 1-2916 
#20	YER070W 500 bp YER070W RNR1 1-2667 ribonucleotide reductase
#21	YER176W 500 bp YER176W ECM32 1-3366 DNA Helicase I
#22	YFL010C_YFL009W 401 bp YFL010C  1-636  YFL009W cdc4 1-2340 beta subunit of large (heterotrimeric) G-proteins (beta-transducin)
#23	YFL036W 500 bp YFL036W RPO41 1-4056 mitochondrial RNA polymerase II
#24	YFR028C 500 bp YFR028C cdc14 1-1656 soluble tyrosine-specific protein phosphatase
#25	YGL058W 425 bp YGL058W rad6 1-519 ubiquitin conjugating (E2) enzyme, separate domains of Rad6p interact with Ubr1 (an E3 ubiquitin ligase needed for multiubiquitination), and Rad18p (a single-stranded DNA-binding protein). The C-terminal 23 residues are critical for sporulation and histone polyubiquitinating activity, but not UV repair or induced mutagenesis.
#26	YGL201C 500 bp YGL201C MCM6 1-3054 
#27	YGR109C 500 bp YGR109C CLB6 1-1143 B-type cyclin
#28	YGR132C_YGR133W 443 bp YGR132C PHB1 1-864 mitochondrial protein, prohibitin homolog\; similar to S. cerevisiae Phb2p YGR133W PEX4 1-552 Member of ubiquitin-conjugating protein family
#29	YGR180C 500 bp YGR180C RNR4 1-1038 Ribonucleotide Reductase
#30	YGR231C_YGR232W 479 bp YGR231C PHB2 1-948 mitochondrial protein, prohibitin homolog\; homolog of mammalian BAP37 and S. cerevisiae Phb1p YGR232W  1-687 
#31	YHR038W 361 bp YHR038W KIM4 1-693 
#32	YHR118C_YHR119W 414 bp YHR118C ORC6 1-1308 50-kDa subunit of ORC YHR119W SET1 1-3243 
#33	YHR164C 500 bp YHR164C DNA2 1-4569 DNA replication helicase
#34	YIL066C 500 bp YIL066C RNR3 1-2610 Ribonucleotide reductase (ribonucleoside-diphosphate reductase) large subunit
#35	YIL139C 500 bp YIL139C rev7 1-738 subunit of DNA polymerase-zeta (Pol-zeta), an enzyme whose sole function appears to be translesion synthesis
#36	YIL150C 299 bp YIL150C DNA43 1-1716 Protein required for S-phase (DNA synthesis) initiation or completion
#37	YIR008C_YIR009W 218 bp YIR008C PRI1 1-1230 p48 polypeptide of DNA primase YIR009W MSL1 1-336 encodes YU2B, a component of yeast U2 snRNP
#38	YJL027C_YJL026W 154 bp YJL027C  1-417  YJL026W rnr2 1-1200 small subunit of ribonucleotide reductase
#39	YJL065C 201 bp YJL065C  1-504 
#40	YJL090C_YJL089W 874 bp YJL090C DPB11 1-2295  YJL089W SIP4 1-2490 shows homology to DNA binding domain of Gal4p, has a leucine zipper motif and acidic region\; lexA-Sip4p activates transcription
#41	YJL173C 500 bp YJL173C RFA3 1-369 subunit 3 of replication factor-A
#42	YJL196C_YJL194W 555 bp YJL196C ELO1 1-933 Elongation enzyme 1, required for the elongation of the saturated fatty acid tetradecanoic acid (14:0) to that of hexadecanoic acid (16:0) YJL194W cdc6 1-1542 Protein involved in initiation of DNA replication
#43	YJR006W 500 bp YJR006W  1-1464 
#44	YJR043C 299 bp YJR043C POL32 1-1053 third (55 kDa) subunit of DNA polymerase delta
#45	YJR067C_YJR068W 198 bp YJR067C YAE1 1-426  YJR068W RFC2 1-1062 Subunit 2 of Replication Factor C\; homologous to human RFC 37 kDa subunit
#46	YKL046C_YKL045W 868 bp YKL046C  1-1350  YKL045W PRI2 1-1587 p58 polypeptide of DNA primase
#47	YKL113C_YKL112W 694 bp YKL113C RAD27 1-1149 42 kDa 5' to 3' exonuclease required for Okazaki fragment processing YKL112W ABF1 1-2196 transcriptional activator and ARS1 binding protein
#48	YLL005C_YLL004W 526 bp YLL005C  1-2607  YLL004W ORC3 1-1851 Third subunit of the origin recognition complex
#49	YLR103C_YLR104W 643 bp YLR103C CDC45 1-1953 omosomal DNA replication initiation protein YLR104W  1-396 
#50	YLR181C_YLR182W 269 bp YLR181C  1-993  YLR182W SWI6 1-2412 regulatory protein
#51	YLR233C_YLR234W 258 bp YLR233C EST1 1-2100 Telomere elongation protein (ever shorter telomeres) YLR234W top3 1-1971 DNA Topoisomerase III
#52	YLR273C_YLR274W 525 bp YLR273C PIG1 1-1947 Protein similar to Gac1p, a putative type 1 protein phosphatase targeting subunit YLR274W CDC46 1-2328 
#53	YML066C_YML065W 676 bp YML066C  1-1110  YML065W ORC1 1-2745 120-kDa (largest) subunit of origin recognition complex (ORC)\; shows homology to Cdc6p, Cdc18p, and Sir3p and to proteins from K. lactis, S. pombe, and humans
#54	YML103C_YML102W 744 bp YML103C NUP188 1-4968 Nucleoporin YML102W CAC2 1-1407 p60 subunit of the yeast omatin Assembly Factor-I (CAF-I)
#55	YMR001C 500 bp YMR001C cdc5 1-2118 protein kinase which functions at the G(sub)2\/M boundary
#56	YMR071C_YMR072W 303 bp YMR071C  1-504  YMR072W ABF2 1-552 HMG-1 homolog, mitochondrial
#57	YMR284W 170 bp YMR284W HDF1 1-1809 DNA binding protein
#58	YNL088W 500 bp YNL088W top2 1-4287 topoisomerase II, Top2p localizes to axial cores in meiosis
#59	YNL102W 333 bp YNL102W pol1 1-4407 DNA polymerase I alpha subunit, p180
#60	YNL261W 219 bp YNL261W ORC5 1-1440 Fifth largest subunit of origin recognition complex\; contains possible ATP-binding site
#61	YNL263C_YNL262W 371 bp YNL263C YIF1 1-945  YNL262W pol2 1-6669 DNA polymerase II
#62	YNL291C_YNL290W 402 bp YNL291C MID1 1-1647 N-glycosylated integral plasma membrane protein YNL290W RFC3 1-1023 Subunit 3 of Replication Factor C\; homologous to human RFC 36 kDa subunit
#63	YNL313C_YNL312W 264 bp YNL313C  1-2715  YNL312W RFA2 1-7, 116-930 subunit 2 of replication factor RF-A\; 29\% identical to the human p34 subunit of RF-A
#64	YOL006C 425 bp YOL006C top1 1-2310 topoisomerase I
#65	YOL094C_YOL093W 259 bp YOL094C RFC4 1-972 Subunit 4 of Replication Factor C\; homologous to human RFC 40 kDa subunit YOL093W  1-882 
#66	YOL095C 236 bp YOL095C  1-2121 
#67	YOL115W 500 bp YOL115W TRF4 1-1755 homologous to Trf5p and Top1p, associates with Smc1p and Smc2p
#68	YOR216C_YOR217W 321 bp YOR216C RUD3 1-1455 Relieves uso1-1 Transport Defect YOR217W RFC1 1-2586 Subunit 1 of Replication Factor C\; homologous to human RFC 140 kDa subunit
#69	YOR330C_YOR332W 192 bp YOR330C mip1 1-3843 catalytic subunit of mitochondrial DNA polymerase YOR332W vma4 1-702 27-kDa subunit of the vacuolar ATPase\; E subunit of V1 sector
#70	YPL167C 230 bp YPL167C rev3 1-4515 DNA polymerase
#71	YPL256C 500 bp YPL256C CLN2 1-1638 G(sub)1 cyclin
#72	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)
#73	YPR019W 453 bp YPR019W CDC54 1-2802 
#74	YPR120C 500 bp YPR120C CLB5 1-1308 B-type cyclin
#75	YPR135W 376 bp YPR135W ctf4 1-2784 DNA polymerase alpha binding protein
#76	YPR162C 340 bp YPR162C ORC4 1-1590 56-kDa subunit of origin recognition complex (ORC)
#77	YPR174C_YPR175W 256 bp YPR174C  1-666  YPR175W DPB2 1-2079 DNA polymerase epsilon, subunit B

#Motif 2
AGACGCGTAA	3	13	1
AAACGCGTAA	20	6	0
AAACGCGTAA	52	198	1
AAACGCGTAA	20	56	1
AAACGCGTAA	6	226	1
AAACGCGTAA	64	413	1
AAACGCGTTA	47	172	1
AAACGCGTTA	49	142	1
AAACGCGTTA	59	123	1
AAACGCGTTA	63	142	1
AGACGCGTCA	3	36	0
AAACGCGTCA	34	311	0
AAACGCGTCA	20	127	1
GGACGCGTAA	20	192	1
GAACGCGTAA	61	254	1
CGACGCGTAA	46	701	0
CGACGCGTAA	47	120	0
CGACGCGTAA	75	251	1
AAACGCGTAT	44	155	1
AGACGCGTTT	13	258	0
AAACGCGTTT	65	128	1
AGACGCGTCT	43	391	1
AGACGCGTGA	1	127	0
GAACGCGTTT	63	154	0
GGACGCGTCT	58	320	1
CGACGCGTAT	49	172	0
GGACGCGTGA	72	334	1
CAACGCGTAT	27	121	1
GAACGCGTGA	72	324	0
CGACGCGTTT	59	158	0
CGACGCGTGA	42	349	0
**********