AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_operons046_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243842
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF0650	135	A. fulgidus predicted coding region AF0650
#1	AF0651	47	A. fulgidus predicted coding region AF0651
#2	AF0776	135	tyrosyl-tRNA synthetase (tyrS)
#3	AF0777	23	translation initiation factor eIF-1A (eif1A)
#4	AF0940	52	DNA topoisomerase VI, subunit A (top6A)
#5	AF1804	50	conserved hypothetical protein
#6	AF2426	85	conserved hypothetical protein

Motif 1
GTAACAGTTAAATAGCATGAGGACAAGACATT	0	60	1
AGGACAAGACATTATCATGAAGTTGATGATTA	0	79	1
AATAATGAGAACTGATAGGAGGTGAGGAAA  	0	115	1
CTTTTTCATCATTAGCAGGTAGCAAGCTTTGG	2	60	1
TTATAAATCTAATGACAGAGTGTGTTC     	5	5	0
GTTTTGGAAGAATGGTAGGAGGGTTAGAGCTA	6	26	1
GGAAACGTCAAATAGCAGATTGCTGAAATAGC	6	60	1
          * ******** *
MAP Score: 4.06806

Motif 2
AGGGGAAAAGTATTAAAGCCTCTTTTGAAC	1	19	1
         GAATTAAAGTTCAAAAGAGGC	1	36	0
TATAAATATATTTTCAAGCCTTTGCAACCT	2	32	1
TGTTTAAATGTTTAAAAGCCCTCCAAAGCT	2	84	0
CCCAGGCTGTTTTTAAAGTTGTTTAAATGT	2	103	0
ATCGCAACGGATTTATAGCCCTTACCAATA	4	20	0
          **********
MAP Score: 3.3498

Motif 3
        ATTACAACTATTGATAATTGCTTATATTTTTACGAT	0	2	1
TTTTTACGATTACAATCATTATGAGTAACAGTTAAATAGCATGA	0	36	1
TTAAGAAGTATAAATATATTTTCAAGCCTTTGCAACCTTTTTCA	2	24	1
TTTAAAGTTGTTTAAATGTTTAAAAGCCCTCCAAAGCTTGCTAC	2	78	0
      CAGATTGAGTTATTGGTAAGGGCTATAAATCCGTTGCG	4	4	1
ACTCTGTCATTAGATTTATAAAATACGGCCCGAAGTTGTACTTT	5	16	1
CTAACCCTCCTACCATTCTTCCAAAACACACATATATTGGTGT 	6	9	0
GTAGGAGGGTTAGAGCTATGGGAAACGTCAAATAGCAGATTGCT	6	40	1
          ** *  * **   **   *    *
MAP Score: 2.16631