AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_operons017_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242991
 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
AAAAAAAGCGTTTAAAATGTTTTCGATGCTGA	0	21	1
CCCTCGAACTTTTTAACTTTTTAGCCAGCTTT	0	59	0
          TTAAAAATCTTTTTTCTCTATT	1	0	1
ATTATTTAATTTTTATGTTTTGACTAATCCAG	4	16	0
TCGATGAAATTTGAAATTATTTAATTTTTATG	4	31	0
ATTTCAGTGAATTTAAATATTG          	5	0	0
TACTCATAACTGGTAACTTTTTGGAAAAGCTT	6	35	0
AATCTTAAACAGTTAATTGTTTAGTTTGATTG	6	118	0
CCGAATATCTTTATAAATGTTGCTGTCGAGGC	6	152	1
CAACTCTGCAATAAATATGTTTCGGCCAAATA	8	32	0
ATGTTAATCCATTTAAATCTTGTGATTACCAT	9	25	1
CCGTGCAGTTTTAAAAGTTTTGGTAACACTGA	9	66	0
          ****** * ***
MAP Score: 6.58859

Motif 3
ATCTTTTTTCTCTATTGAAGGTTGCCTTAG	1	16	1
       GGTTTTATTTCAAGTACAAAAAC	2	3	1
GTAAGGGAACTCTATTTCAACTCGAAAAAT	2	37	1
 GGTGGGAGTTTGATTTCAGGTGTAATAAA	2	82	0
AATTTCAAATTTCATCGAAGCT        	4	45	1
CTTCTCCCTTCCTATTTCAGTGAATTTAAA	5	15	0
AAGATGCACTTGTATTTAAGCTTTTCCAAA	6	18	1
TTATGGTAAAAGCATTGCAACTTAGTTGCA	6	90	1
ATTGTTTAGTTTGATTGCAACTAAGTTGCA	6	105	0
TCACTTTTATTGTATCGCAGTAACCCGCAA	7	115	0
GCCTAACTCGTGCATTTCCGTAGGTATGCC	7	189	0
CTTCGTCATCACTATTTCAAGCGCTGATTT	7	219	0
CCGAAACATATTTATTGCAGAGTTGAGAAG	8	39	1
AGGATGTTAATCCATTTAAATCTTGTGATT	9	22	1
          **********
MAP Score: 6.5864

Motif 4
TGCGTGGACTTCATCACCTTCTTTGGGAGGT	7	58	1
ATCAACCGCATTATCAACCACCTCCCAAAGA	7	77	0
CGCAAGGGCCTCATCAACCGCATTATCAACC	7	89	0
         TTTATCAAACTCAAAAATGTAT	8	1	1
GTGATTACCATCATCACATATCAGTGTTACC	9	46	1
ATCACCTCCTTCATCAAATCATCATTCATCG	9	114	0
         GTCATCACCTCCTTCATCAAAT	9	126	0
          ********* *
MAP Score: 6.30131

Motif 5
        TCGAAGCTGTAAGGAAGAGGCCTGGAATGTA	7	2	1
CGGCATCGGTAGAGGATAACGGGCGAGGCATACCTACGG	7	163	1
TAAATTCACTGAAATAGGAAGGGAGAAGG          	5	17	1
GAGGTGGTTGATAATGCGGTTGATGAGGCCCTTGCGGGT	7	84	1
          GAAAAAAGTTGGTCGGGGGAATATAAACT	3	14	0
ATCAGCGCTTGAAATAGTGATGACGAAGCTTCACGCTGG	7	221	1
TCACGCTGGGGGAAAGTTCTCGAAGAAGGTTTACCGCGT	7	251	1
AATATCTTTATAAATGTTGCTGTCGAGGCGGGGGC    	6	155	1
AAAAAGTTAAAAAGTTCGAGGGATTAGGGAGGAT     	0	69	1
GCATACCTACGGAAATGCACGAGTTAGGCAAATCAGCGC	7	190	1
AGAGCCGATGAATGATGATTTGATGAAGGAGGTGATGAC	9	109	1
TCTCAACTCTGCAATAAATATGTTTCGGCCAAATAATAC	8	28	0
          * **      **  *****
MAP Score: 6.26431

Motif 6
TTGAGGTGTCAGCATCGAAAACATTTTAAACGCTTTTTTT	0	21	0
TGACACCTCAAAGCTGGCTAAAAAGTTAAAAAGTTCGAGG	0	50	1
TTGCCTTAGGGCTATTTTAAAAAGCAAAAACAAAGTG   	1	37	1
  CGGAGGCTGGATTAGTCAAAACATAAAAATTAAATAAT	4	8	1
          AGCTTCGATGAAATTTGAAATTATTTAATT	4	37	0
ATAACTGGTAACTTTTTGGAAAAGCTTAAATACAAGTGCA	6	22	0
AAGTTGCAATGCTTTTACCATAATATGAAATTGTACCAAA	6	73	0
CATTTATAAAGATATTCGGAAAATCTTAAACAGTTAATTG	6	131	0
ATATGTGATGATGGTAATCACAAGATTTAAATGGATTAAC	9	27	0
ATCACATATCAGTGTTACCAAAACTTTTAAAACTGCACGG	9	58	1
          *   *    ****  * ***
MAP Score: 6.05502

Motif 7
AAGTTAAAAAGTTCGAGGGATTAGGGAGGAT	0	72	1
AAAAACGTTTGTAAGGGAACTCTATTTCAAC	2	27	1
GAAAAAAGTTGGTCGGGGGAATATAAACTTA	3	12	0
CACTGAAATAGGAAGGGAGAAGG        	5	23	1
GAAGCTGTAAGGAAGAGGCCTGGAATGTATA	7	12	1
TGGAGTAGGAGTGCGTGGACTTCATCACCTT	7	47	1
AGAGGATAACGGGCGAGGCATACCTACGGAA	7	173	1
GAAGCTTCACGCTGGGGGAAAGTTCTCGAAG	7	245	1
TTTACCGCGTTTCCGGGGGCTTGCACGGAG 	7	280	1
TTTTAAAACTGCACGGGGAATTAGGGAAGAG	9	82	1
          ** ********
MAP Score: 2.43224

Motif 8
        GCTGGCTTTACAAAAAAAGCGTTTAAAATG	0	2	1
TTTTCGATGCTGACACCTCAAAGCTGGCTAAAAAGTTA	0	40	1
AAATCTTTTTTCTCTATTGAAGGTTGCCTTAGGGCTAT	1	14	1
CACTTTGTTTTTGCTTTTTAAAATAGCCCTAAGGCAAC	1	36	0
ACAAACGTTTTTGTACTTGAAATAAAACC         	2	1	0
GGGAACTCTATTTCAACTCGAAAAATGCAGGTTTGGAT	2	41	1
GATACTTTTATTACACCTGAAATCAAACTCCCACC   	2	76	1
ACTAAACAATTAACTGTTTAAGATTTTCCGAATATCTT	6	125	1
ATTTTCCGAATATCTTTATAAATGTTGCTGTCGAGGCG	6	147	1
AATAAAAGTGAGTCTTCACAAAGATGGCTCGGCATCGG	7	134	1
AGTGTTACCAAAACTTTTAAAACTGCACGGGGAATTAG	9	68	1
          *  ** ** ***  *  *
MAP Score: 1.38298