AlignACE 3.0 10/20/99
AlignACE2 -i TP/TP_operons028_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944239978
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TP0267	300	conserved hypothetical protein
#1	TP0270	73	polynucleotide adenylyltransferase (pcnA)
#2	TP0437	29	T. pallidum predicted coding region TP0437
#3	TP0496	91	conserved hypothetical protein
#4	TP0596	107	polynucleotide adenylyltransferase (pcnB)

Motif 1
GATGATACTGCTCCTTCGCGGGAAAGTAGG	0	211	1
CTTCACCCTACCCCTTTGCGTAAAATATTT	0	110	1
TAGCCAGGCTCCCCTTTGCCCATCACTCGC	0	244	1
AAGTCAAGCTCTCCTACGCCGATGATACTG	0	191	1
TGACAGGGAGCTCCTTCTCGGGGGAGGATG	4	77	1
ATTCATCCTTCTCCTTCACCCTACCCCTTT	0	97	1
AACAATGAATCTCCACTGCGAATCAGAAAC	1	10	0
GGATCGGAATATCCTTTGCTGCTCGATC  	3	8	0
ACGGGTATGACCTCTCCACCATGGCAACCA	0	144	0
  CTACCCCGCCCATCCTCCCCCGAGAAGG	4	89	0
          **********
MAP Score: 16.8862

Motif 2
TATTCATCCTTCTCCTTCACCCTACCCCTTT	0	96	1
GGGTATGACCTCTCCACCATGGCAACCAGGC	0	141	0
CGGAAGTCAAGCTCTCCTACGCCGATGATAC	0	188	1
CGATGATACTGCTCCTTCGCGGGAAAGTAGG	0	210	1
TAGTAGCCAGGCTCCCCTTTGCCCATCACTC	0	241	1
CAACAATGAATCTCCACTGCGAATCAGAAAC	1	10	0
CCTTCCTCACGCTCTACTGCATGCTCGTTTT	1	48	0
TTGACAGGGAGCTCCTTCTCGGGGGAGGATG	4	76	1
          ***** *****
MAP Score: 10.1635

Motif 3
CTTCTCCTTCACCCTACCCCTTTGCGTAAAATAT	0	104	1
ACGGGTATGACCTCTCCACCATGGCAACCAGGCG	0	140	0
AAGTCAAGCTCTCCTACGCCGATGATACTGCTCC	0	191	1
TACGCCGATGATACTGCTCCTTCGCGGGAAAGTA	0	205	1
GGGAGCCTGGCTACTACCTACTTTCCCGCGAAGG	0	223	0
      GTTTCTGATTCGCAGTGGAGATTCATTG	1	4	1
TCCTCACGCTCTACTGCATGCTCGTTTTTTTCTA	1	42	0
GTATTTTGTAATTCGGCACGGTGGTATGAATGCT	4	30	1
GGTGGTATGAATGCTTCCTAGTTGGTCTTGACAG	4	49	1
TGACAGGGAGCTCCTTCTCGGGGGAGGATGGGCG	4	77	1
          ** ** * ** ***
MAP Score: 5.81489

Motif 4
CAGCCTATCGACCTTGTAGTGT        	0	2	0
ATATTATTCATCCTTCTCCTTCACCCTACC	0	92	1
TCGCCTGGTTGCCATGGTGGAGAGGTCATA	0	139	1
GAGCTTGACTTCCGTGTTCGGGATGGGAAC	0	172	0
AGTCAAGCTCTCCTACGCCGATGATACTGC	0	192	1
ATGATACTGCTCCTTCGCGGGAAAGTAGGT	0	212	1
        GCTCCTTGCAGGTAACTGCGCC	2	17	0
TATGAATGCTTCCTAGTTGGTCTTGACAGG	4	54	1
GAGAAGGAGCTCCCTGTCAAGACCAACTAG	4	66	0
GACAGGGAGCTCCTTCTCGGGGGAGGATGG	4	78	1
          **********
MAP Score: 2.42774