AlignACE 3.0 10/20/99
AlignACE2 -i TH/TH_operons064_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944246239
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MTH890	145	conserved protein
#1	MTH891	59	conserved protein
#2	MTH892	21	ATP-dependent protease LA related protein
#3	MTH893	60	integrase-recombinase protein
#4	MTH894	179	conserved protein
#5	MTH895	51	conserved protein
#6	MTH898	22	conserved protein
#7	MTH1795	72	transcriptional regulator

Motif 1
TATTATGATAACATAGATATTTAAATATAGCCCAGAA	0	42	1
TATAGCCCAGAAACACACCTCTGATTATTTTATATAT	0	67	1
          ATCTGGCCCTTTAATAACTTGATAATA	0	128	0
TGTTATCATCACACTTCAATTTGATAACCAGTCATTC	1	14	1
       GTAAACCCTCCTTTTGAGGAATGACTGGTT	1	39	0
TGAAAAATTAAGCCCGCCCTTGAAGGAAGAATTCAGG	4	64	0
TCGATGAAGTCACTGACCTTCTGAAAAATTAAGCCCG	4	85	0
TTACCTTTATATCCATAAATTTGAATATATTGA    	4	156	1
  TTTAATCCATCCGAATATTTCACCAGAGTCTCTGC	7	8	1
          * **  *  *****  *
MAP Score: 4.23892

Motif 2
TAACAGATTCATGGAGGAAAG          	0	0	0
TATAAAATAATCAGAGGTGTGTTTCTGGGCT	0	70	0
TGGTTATCAAATTGAAGTGTGATGATAACAG	1	13	0
AAACCCTCCTTTTGAGGAATGACTGGTTATC	1	36	0
ATCAGATGAGTTCGATGAGTGCATGATCCGC	3	20	1
CAACCTGGAATTTGAGGTGAA          	5	40	1
 CAGCACCCTAAGGAGGTATGAT        	6	9	1
          ** ********
MAP Score: 3.21967

Motif 3
      CTTTCCTCCATGAATCTGTTAAAATGATATAG	0	4	1
   ATCTGGCCCTTTAATAACTTGATAATATCTATATC	0	120	0
ACCAGTCATTCCTCAAAAGGAGGGTTTAC         	1	40	1
CTGAATTCTTCCTTCAAGGGCGGGCTTAATTTTTCAGA	4	65	1
      TTCACCTCAAATTCCAGGTTGAACCTGTTAAC	5	29	0
          ***  ** *   ** * *
MAP Score: 1.79129

Motif 4
TAGTATTATGATAACATAGATATTTAAATATAGC	0	39	1
AGAGGTGTGTTTCTGGGCTATATTTAAATATCTA	0	55	0
ACACCTCTGATTATTTTATATATCAGTATCGTCA	0	81	1
TAATAACTTGATAATATCTATATCTTATATGACG	0	110	0
ATCATCACACTTCAATTTGATAACCAGTCATTCC	1	18	1
ATCCGCAAGGTTTAAGTGGATATTT         	3	45	1
 TTAATTTATTTTTCATTTATTTCAATAAAATTC	4	9	1
GCAATCCCAATTTACCTTTATATCCATAAATTTG	4	145	1
          ** *  * ******
MAP Score: 1.69961

Motif 5
CAAGTTATTAAAGGGCCAGAT         	0	134	1
ACTTCAATTTGATAACCAGTCATTCCTCAA	1	26	1
TGAGTTCGATGAGTGCATGATCCGCAAGGT	3	26	1
AATTCAGGTCAGGAGCCAGAAGATTGCCTG	4	38	1
GGAGCCAGAAGATTGCCTGAATTCTTCCTT	4	49	1
GGTAAATTGGGATTGCCAGTATATATAACT	4	131	0
          **********
MAP Score: 0.942929