AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID037_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943391191
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	queA	92	synthesis of queuine in tRNA; probably S-adenosylmethionine:tRNA ribosyltransferase-isomerase
#1	tgt	55	tRNA-guanine transglycosylase
#2	yajC	22	orf, hypothetical protein
#3	secD	27	protein secretion; membrane protein, part of the channel

Motif 1
AGGGAGAGCGCCCCGGCACTAGACTACCCG	0	45	1
GCACTAGACTACCCGCCTCTTATTTTAGTC	0	60	1
        TTCCGCGGCGCTGGTTTAAAAC	1	2	1
          **********
MAP Score: 3.68076

Motif 2
TAGTCTAGTGCCGGGGCGCTCTCCCTGCAA	0	41	0
ACTAGACTACCCGCCTCTTATTTTAGTCTG	0	62	1
        TTCCGCGGCGCTGGTTTAAAAC	1	2	1
          **********
MAP Score: 1.06238

Motif 3
GGGAGAGCGCCCCGGCACTAGACTACCCGCCTCT	0	46	1
CACTAGACTACCCGCCTCTTATTTTAGTCTGAGT	0	61	1
       TTCCGCGGCGCTGGTTTAAAACGTTGG	1	3	1
TGGTTTAAAACGTTGGACTGTTTTTCTGACGTAG	1	21	1
          ****** **   **
MAP Score: 0.914554