AlignACE 3.0 10/20/99
AlignACE2 -i TP/TP_operons023_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944239750
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TP0298	132	exported protein (tpn38b)
#1	TP0319	28	membrane lipoprotein (tmpC)
#2	TP0321	75	ribose/galactose ABC transporter, ATP-binding protein (rbsA-2)

Motif 1
CAATGCGTTTGGGGGCAGGGGTGAGGAGTA	0	35	1
TAATGAACTTGAGGGAGGGGCT        	2	63	1
AGGGATTTTTGGGGGGAGGTGTT       	0	119	1
TGTCGATAAAGGGGGGAGGATTCTT     	1	13	1
CCCACTGACCACGGGCGGGTCGAGACACAC	2	18	0
CACCCTACGCGAGAGAGGGATTTTTGGGGG	0	104	1
TTCAGGCTGTGGGTGCCGGTAGGGTGCACC	0	78	1
GCACCACCCAGAGAGAAGGAGAAAGA    	0	6	0
        AGTGGGGCGTGTGTCTCGACCC	2	2	1
          **********
MAP Score: 19.6367

Motif 2
GAGAGGGATTTTTGGGGGGAGGTGTT      	0	116	1
GTTTGTCGATAAAGGGGGGAGGATTCTT    	1	10	1
GTGCAATGCGTTTGGGGGCAGGGGTGAGGAGT	0	32	1
AGTAATGAACTTGAGGGAGGGGCT        	2	61	1
ATACCCACTGACCACGGGCGGGTCGAGACACA	2	19	0
GCCCGTGGTCAGTGGGTATGGGGACGTCCAGT	2	32	1
TCTGGTCTTTTCAGGCTGTGGGTGCCGGTAGG	0	69	1
TCTCCTTCTCTCTGGGTGGTGCAATGCGTTTG	0	14	1
GGTGCACCCTACGCGAGAGAGGGATTTTTGGG	0	100	1
AGGCTGTGGGTGCCGGTAGGGTGCACCCTACG	0	81	1
          *  *********
MAP Score: 13.5564

Motif 3
CCTTCTCTCTGGGTGGTGCAATGCGTTTGGG	0	17	1
GTGCAATGCGTTTGGGGGCAGGGGTGAGGAG	0	32	1
TTTGGGGGCAGGGGTGAGGAGTAGTGCTCTG	0	42	1
CTTTTCAGGCTGTGGGTGCCGGTAGGGTGCA	0	75	1
AGAGGGATTTTTGGGGGGAGGTGTT      	0	117	1
TGTCGATAAAGGGGGGAGGATTCTT      	1	13	1
TGGTCAGTGGGTATGGGGACGTCCAGTAATG	2	37	1
GTAATGAACTTGAGGGAGGGGCT        	2	62	1
          ********* *
MAP Score: 9.2006

Motif 4
ACTCCTCACCCCTGCCCCCAAACGCATTGCA	0	33	0
GTGCACCCTACCGGCACCCACAGCCTGAAAA	0	76	0
GTGCCGGTAGGGTGCACCCTACGCGAGAGAG	0	90	1
     AACACCTCCCCCCAAAAATCCCTCTC	0	116	0
    AAGAATCCTCCCCCCTTTATCGACAAA	1	11	0
GGCGGGTCGAGACACACGCCCCACT      	2	4	0
ACTGGACGTCCCCATACCCACTGACCACGGG	2	33	0
         AGCCCCTCCCTCAAGTTCATTA	2	63	0
          *** *******
MAP Score: 3.52542

Motif 5
       TCTTTCTCCTTCTCTCTGGGTGGT	0	3	1
CTCACCCCTGCCCCCAAACGCATTGCACCAC	0	29	0
AGAGCACTACTCCTCACCCCTGCCCCCAAAC	0	41	0
ACCCTACCGGCACCCACAGCCTGAAAAGACC	0	72	0
CGTAGGGTGCACCCTACCGGCACCCACAGCC	0	82	0
CCCCAAAAATCCCTCTCTCGCGTAGGGTGCA	0	102	0
      AACACCTCCCCCCAAAAATCCCTCT	0	117	0
AAGAATCCTCCCCCCTTTATCGACAAAC   	1	7	0
GGGTCGAGACACACGCCCCACT         	2	1	0
GGGGCGTGTGTCTCGACCCGCCCGTGGTCAG	2	13	1
GACGTCCCCATACCCACTGACCACGGGCGGG	2	29	0
         AGCCCCTCCCTCAAGTTCATTA	2	63	0
          ********* *
MAP Score: 2.98272