AlignACE 3.0 10/20/99
AlignACE2 -i AA/AA_fusions007_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944234491
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	pyrD	125	dihydroorotase dehydrogenase
#1	dmsB2	232	dimethylsulfoxide reductase chain B
#2	rpmJ	60	ribosomal protein L36
#3	secY	44	preprotein translocase SecY
#4	lysR2	50	transcriptional regulator (LysR family)
#5	fdoG	212	formate dehydrogenase alpha subunit
#6	cysM	41	cysteine synthase, O-acetylserine (thiol) lyase B
#7	aq_1558	27	putative protein
#8	gltB	30	glutamate synthase large subunit
#9	gltD	39	glutamate synthase small subunit gltD

Motif 1
TACTCGGCGGTGAAAATTTTTATAAAAATT	0	53	1
AATATTGTTTTGAAAATTTTGTCTTTTTTT	5	134	1
CTTTATTATATTAAAATCTTTTAAC     	3	29	1
      AACTTGAATATCTTAAAGGAGAGT	9	4	1
AATTATTCAATGAAAATGTTCGAAAAA   	5	7	0
ATGCCTATTTTTAAAATATTGTTTTGAAAA	5	120	1
ATAAAACTCGTTAAAGTCTTCATTCAGCTC	1	15	1
CCACAATAGCGGAATATCTTAGTATAACCT	2	31	0
AATAGGCATATGAACATTTTTTTATTGTGT	5	99	0
TTTCAAATCATGAAAAAATTTAAAAAAAAG	5	156	0
TCCGAGACCTTTAAAATAGTATCATACCGC	6	18	1
GAGCCGATAAGGAAAGTCGTAAAACCGATT	1	147	1
ATATTGCATGTTAATAAATTCCTTATATTC	5	61	0
          **********
MAP Score: 12.1709

Motif 2
AAGTAAACCAAACTATATTTTACTACTCGGCG	0	30	1
CTCGGCGGTGAAAATTTTTATAAAAATTTCGT	0	55	1
TTTTTATAAAAATTTCGTTATATATACATAAA	0	69	1
         CAAGTTTATTTTAACTTCCTAAC	0	112	0
CCTCCGAGAGAACTTTATTATATTAAAATCTT	3	17	1
      AGCTTATATTCTCTTATCATCTCTTT	4	4	1
   TTTTTCGAACATTTTCATTGAATAATTAA	5	7	1
GCATGTTAATAAATTCCTTATATTCAAATATC	5	54	0
TAGGCATATGAACATTTTTTTATTGTGTATCA	5	95	0
CTATTTTTAAAATATTGTTTTGAAAATTTTGT	5	124	1
TTGTTTTGAAAATTTTGTCTTTTTTTTAAATT	5	138	1
CTTTTTTTTAAATTTTTTCATGATTTGAAAGG	5	156	1
AGACCTTTAAAATAGTATCATACCGCCCT   	6	22	1
         TAAGTTTTTATTAGAATATCCTA	7	1	1
          ** *** *****
MAP Score: 10.7771

Motif 3
        AATACCACCTCCTGAAATTTAA	0	2	1
TTATAAAAATTTTCACCGCCGAGTAGTAAA	0	48	0
 CAAGTTTATTTTAACTTCCTAACCTTTAA	0	106	0
TCCTCATCCTTCTTACTTTCATTCACGCAC	1	43	1
TACCAGTAAATTTTACTTCTCCTTACCTCG	1	89	0
CCTTATACTCTCTATCCTCCTGAGGATACT	1	209	1
        TCTTCTACCTCCGAGAGAACTT	3	2	1
         TTTCTACCTCCGAGACCTTTA	6	1	1
TAAAATAGTATCATACCGCCCT        	6	29	1
          **********
MAP Score: 5.93601

Motif 4
     AATACCACCTCCTGAAATTTAAGTA	0	5	1
CATTCAGCTCCTCATCCTTCTTACTTTCAT	1	35	1
GTAAATTTTACTTCTCCTTACCTCGGGAAA	1	84	0
GCATTGACTTTTCCCCCTTAATACTTATCC	1	181	1
CCCCTTAATACTTATCCTTATACTCTCTAT	1	194	1
TATACTCTCTATCCTCCTGAGGATACTCAG	1	212	1
         TCTTCTACCTCCGAGAGAACT	3	1	1
TTTTTAGTTTATTCCCCTTTCAAATCATGA	5	173	0
          TTTCTACCTCCGAGACCTTT	6	0	1
TTAAAATAGTATCATACCGCCCT       	6	28	1
          **********
MAP Score: 0.0760226