AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_operons017_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242976
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF0238	93	centromere/microtubule-binding protein (cbf5)
#1	AF0481	64	proteasome, subunit beta (psmB)
#2	AF0483	101	conserved hypothetical protein
#3	AF0484	33	GTP cyclohydrolase II (ribA-1)
#4	AF0487	57	penicillin G acylase
#5	AF0527	36	translation initiation factor eIF-2, subunit alpha (eif2A)
#6	AF0528	180	cytochrome-c3 hydrogenase, subunit gamma
#7	AF0530	300	DNA gyrase, subunit B (gyrB)
#8	AF0532	68	mRNA 3'-end processing factor, putative
#9	AF0764	138	LSU ribosomal protein L7AE (rpl7AE)

Motif 1
TTAAAAAGTTCGAGGGATTAGGGAGGAT    	0	75	1
          GGTGGGAGTTTGATTTCAGGTG	2	89	0
AAAAGTTGGTCGGGGGAATATAAACTTAAT  	3	8	0
      CGGAGGCTGGATTAGTCAAAACATAA	4	4	1
     AGCTTCGATGAAATTTGAAATTATTTA	4	40	0
TATTTAAATTCACTGAAATAGGAAGGGAGAAG	5	13	1
GAATGTATATCGGTGGAGTAGGAGTGCGTGGA	7	34	1
GTTGATAATGCGGTTGATGAGGCCCTTGCGGG	7	90	1
TAAAACTGCACGGGGAATTAGGGAAGAGCCGA	9	85	1
AGGGAAGAGCCGATGAATGATGATTTGATGAA	9	104	1
AATGATGATTTGATGAAGGAGGTGATGAC   	9	119	1
          ** **** ****
MAP Score: 10.9926

Motif 2
ATGCTGACACCTCAAAGCTGGCTAAAAAGTT	0	46	1
TCTATTTCAACTCGAAAAATGCAGGTTTGGA	2	47	1
AAGGTTTGTACTCATAACTGGTAACTTTTTG	6	44	0
TCAACCACCTCCCAAAGAAGGTGATGAAGTC	7	64	0
AGTGAGTCTTCACAAAGATGGCTCGGCATCG	7	140	1
GGGGAAAGTTCTCGAAGAAGGTTTACCGCGT	7	259	1
 TTTATCAAACTCAAAAATGTATTATTTGGC	8	9	1
          * *********
MAP Score: 6.48076

Motif 3
CTTTGAGGTGTCAGCATCGAAAACATTTTAAACGCTT	0	26	0
CAAAGCTGGCTAAAAAGTTAAAAAGTTCGAGGGATTA	0	58	1
AAGGCAACCTTCAATAGAGAAAAAAGATTTTTAA   	1	7	0
AGGGCTATTTTAAAAAGCAAAAACAAAGTG       	1	44	1
 GGTTTTATTTCAAGTACAAAAACGTTTGTAAGGGAA	2	9	1
GAACTCTATTTCAACTCGAAAAATGCAGGTTTGGATA	2	43	1
GCTGGATTAGTCAAAACATAAAAATTAAATAATTTCA	4	15	1
TTAGTTGCAATCAAACTAAACAATTAACTGTTTAAGA	6	111	1
      TTTATCAAACTCAAAAATGTATTATTTGGCC	8	4	1
          ****     **** * *
MAP Score: 5.38907

Motif 4
TGGCTTTACAAAAAAAGCGTTTAAAATGTTTTCGA	0	12	1
CTCAAAGCTGGCTAAAAAGTTAAAAAGTTCGAGGG	0	56	1
TTCAATAGAGAAAAAAGATTTTTAA          	1	0	0
TATTTCAAGTACAAAAACGTTTGTAAGGGAACTCT	2	15	1
GGCTGGATTAGTCAAAACATAAAAATTAAATAATT	4	14	1
AAACATAAAAATTAAATAATTTCAAATTTCATCGA	4	28	1
GTAACTTTTTGGAAAAGCTTAAATACAAGTGCATC	6	20	0
CAGTTATGAGTACAAACCTTTGGTACAATTTCATA	6	55	1
TCATATTATGGTAAAAGCATTGCAACTTAGTTGCA	6	85	1
AAAGATATTCGGAAAATCTTAAACAGTTAATTGTT	6	129	0
AAAATAGGATGTTAATCCATTTAAATCTTGTGATT	9	17	1
TATCAGTGTTACCAAAACTTTTAAAACTGCACGGG	9	64	1
          *  *** ****  **
MAP Score: 3.66229

Motif 5
TAAAATGTTTTCGATGCTGACACCTCAAAG	0	33	1
TGCTGACACCTCAAAGCTGGCTAAAAAGTT	0	47	1
          CGGAGGCTGGATTAGTCAAA	4	0	1
AATGTTGCTGTCGAGGCGGGGGC       	6	167	1
          TCGAAGCTGTAAGGAAGAGG	7	0	1
CAACCACCTCCCAAAGAAGGTGATGAAGTC	7	64	0
GTGAGTCTTCACAAAGATGGCTCGGCATCG	7	141	1
TTATCCTCTACCGATGCCGAGCCATCTTTG	7	152	0
GGGAAAGTTCTCGAAGAAGGTTTACCGCGT	7	260	1
TAGGGAAGAGCCGATGAATGATGATTTGAT	9	103	1
GAATGATGATTTGATGAAGGAGGTGATGAC	9	118	1
          **********
MAP Score: 2.84291

Motif 6
AGGTGTCAGCATCGAAAACATTTTAAACGCTTTTTTT	0	21	0
CACCTCAAAGCTGGCTAAAAAGTTAAAAAGTTCGAGG	0	53	1
CCTTAGGGCTATTTTAAAAAGCAAAAACAAAGTG   	1	40	1
       GGTTTTATTTCAAGTACAAAAACGTTTGTA	2	3	1
GTTTGGATACTTTTATTACACCTGAAATCAAACTCCC	2	71	1
GGAGGCTGGATTAGTCAAAACATAAAAATTAAATAAT	4	11	1
       AGCTTCGATGAAATTTGAAATTATTTAATT	4	37	0
ACTGGTAACTTTTTGGAAAAGCTTAAATACAAGTGCA	6	22	0
AGTACAAACCTTTGGTACAATTTCATATTATGGTAAA	6	63	1
TTATAAAGATATTCGGAAAATCTTAAACAGTTAATTG	6	131	0
          TTTATCAAACTCAAAAATGTATTATTT	8	0	1
AAAAAATAGGATGTTAATCCATTTAAATCTTGTGATT	9	15	1
CATATCAGTGTTACCAAAACTTTTAAAACTGCACGGG	9	62	1
          **    ****  * ***
MAP Score: 1.4892

Motif 7
AAATAGCCCTAAGGCAACCTTCAATAGAGAAAAAAG	1	18	0
AGGTTGCCTTAGGGCTATTTTAAAAAGCAAAAACAA	1	34	1
CAACTCGAAAAATGCAGGTTTGGATACTTTTATTAC	2	54	1
TGGGAGTTTGATTTCAGGTGTAATAAAAGTATCCAA	2	73	0
ATTAGTCAAAACATAAAAATTAAATAATTTCAAATT	4	20	1
ATGCACTTGTATTTAAGCTTTTCCAAAAAGTTACCA	6	21	1
CCCCGCCTCGACAGCAACATTTATAAAGATATTCGG	6	152	0
GATACAATAAAAGTGAGTCTTCACAAAGATGGCTCG	7	129	1
CACTATTTCAAGCGCTGATTTGCCTAACTCGTGCAT	7	204	0
AAACATATTTATTGCAGAGTTGAGAAGTCAATAAGT	8	42	1
CCATCATCACATATCAGTGTTACCAAAACTTTTAAA	9	53	1
          *  ****  ** * **
MAP Score: 1.00024