AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_operons026_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944252593
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM1043	46	histidyl-tRNA synthetase-related protein
#1	TM1044	300	transposase, IS605-TnpB family
#2	TM1131	155	aminotransferase, putative

Motif 1
CATGAAAATGTTTTTCGGTGAACACCACCAT	1	22	1
CTTTGCGGTTTTATTCGATAAACAAAAAGGC	1	129	0
AGAAGACACCATTTTCTATAAGGTGGGGATG	1	158	1
ATCTTCTTCATTTCTCTATGATATATTAACA	1	215	0
ATTTGATGTATTCTTTTAACACTTCCAAAGG	1	270	0
AGTATACCAGTTTTTCTATCAAATTCTCAAT	2	49	1
AAATTCTCAATTTTTCGAATACACGTTGAAT	2	69	1
GGAATATCTTTTCTTCTGAAAAATTATACAC	2	127	0
          ********* *
MAP Score: 5.99047

Motif 2
       CTCCCCAGTGAACTACCATGACTTATAG	0	28	0
AAATGTTTTTCGGTGAACACCACCATCATTGCTAC	1	27	1
TTGCTACGGCCCGGCGGTTTCTCCACCGGGTGTGT	1	55	1
TCGACGTGGCCCGTGCGATCTCCCACCATCACACA	1	85	0
          CCGAGGATCCCTCCAGATAGAAGTA	2	0	1
          *** * *  ** ***
MAP Score: 3.92438

Motif 3
AGCCATGACTTCTATAAGTCATGGTAGTTCACTG	0	17	1
ACCACCATCATTGCTACGGCCCGGCGGTTTCTCC	1	45	1
CCCGGCGGTTTCTCCACCGGGTGTGTGATGGTGG	1	64	1
ACGGGCCACGTCGAGAAGACGTGGCCTTTTTGTT	1	106	1
AAGACACCATTTTCTATAAGGTGGGGATGAATTT	1	160	1
AGATTGTCTTTTGACAGTAGGCGGATCACCTTTG	1	242	1
      GTCCTTGAGATTTGATGTATTCTTTTAA	1	282	0
ATTCTCAATTTTTCGAATACACGTTGAATTTTAA	2	71	1
TGCAGAAATTTCGCCAGTACTGGTGTATAATTTT	2	105	1
          ******   * ***
MAP Score: 1.79401

Motif 4
GGCCCGGCGGTTTCTCCACCGGGTGTGTGATGGTGGGAGATCGC	1	62	1
GGCCTTTTTGTTTATCGAATAAAACCGCAAAGAAGACACCATTT	1	128	1
AGAAGACACCATTTTCTATAAGGTGGGGATGAATTTGCAATTTA	1	158	1
ATCTTCTTCATTTCTCTATGATATATTAACATTTTGGCACATAT	1	202	0
AGTATACCAGTTTTTCTATCAAATTCTCAATTTTTCGAATACAC	2	49	1
AAATTCTCAATTTTTCGAATACACGTTGAATTTTAATGCAGAAA	2	69	1
AATGCAGAAATTTCGCCAGTACTGGTGTATAATTTTTCAGAAGA	2	103	1
          *** ** *  *     * *    *
MAP Score: 1.69251

Motif 5
CTTATAGAAGTCATGGCTTCCCGCT       	0	3	0
CAGTGAACTACCATGACTTATAGAAGTCATGG	0	19	0
TGCTACGGCCCGGCGGTTTCTCCACCGGGTGT	1	56	1
TCGACGTGGCCCGTGCGATCTCCCACCATCAC	1	88	0
AACAAAAAGGCCACGTCTTCTCGACGTGGCCC	1	108	0
TTATAGAAAATGGTGTCTTCTTTGCGGTTTTA	1	147	0
CCTTGAGATTTGATGTATTCTTTTAACACTTC	1	276	0
TTCGAATACACGTTGAATTTTAATGCAGAAAT	2	82	1
ACACCAGTACTGGCGAAATTTCTGCATTAAAA	2	99	0
          *****  *****
MAP Score: 0.72597

Motif 6
CGGATCACCTTTGGAAGTGTTAAAAGAATAC	1	263	1
ATCCCTCCAGATAGAAGTATTTGCATACTTC	2	16	1
ACTGGTATACTTTGAAGTATGCAAATACTTC	2	29	0
GTCCTTGAGATTTGATGTATTCTTTTAACAC	1	279	0
CGTAGCAATGATGGTGGTGTTCACCGAAAAA	1	32	0
TCAACGTGTATTCGAAAAATTGAGAATTTGA	2	67	0
GGATGCAATCATGAAAATGTTTTTCGGTGAA	1	13	1
TTAATATATCATAGAGAAATGAAGAAGATTG	1	217	1
GAATTTGCAATTTAATATGTGCCAAAATGTT	1	188	1
          ** ********
MAP Score: 0.387877