AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_operons026_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944252586
 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
CATGAAAATGTTTTTCGGTGAACACCACCATCATTGCTAC	1	22	1
GGCCTTTTTGTTTATCGAATAAAACCGCAAAGAAGACACC	1	128	1
GAGATTTGATGTATTCTTTTAACACTTCCAAAGGTGATCC	1	264	0
ACCTTTGGAAGTGTTAAAAGAATACATCAAATCTCAAGGA	1	269	1
GGTATACTTTGAAGTATGCAAATACTTCTATCTGGAGGGA	2	17	0
CCTCCAGATAGAAGTATTTGCATACTTCAAAGTATACCAG	2	19	1
          *   **    ** ** ** *
MAP Score: 2.6029

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