AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID117_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943391941
 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	ruvA	175	Holliday junction helicase subunit B; branch migration; repair
#3	ruvC	34	Holliday junction nuclease; resolution of structures; repair
#4	yebC	28	orf, hypothetical protein
#5	ntpA	117	dATP pyrophosphohydrolase

Motif 1
TAGTCTAGTGCCGGGGCGCTCTCCCTGCAA	0	41	0
AGACTAAAATAAGAGGCGGGTAGTCTAGTG	0	61	0
        TTCCGCGGCGCTGGTTTAAAAC	1	2	1
TTTCAGTTCATCGAGACACCTCGCAAGTTT	2	75	1
AACAGCAAAACGGAGACGCGTG        	3	22	1
TCGCGTTGCATCGAGGCGGCAACTGAGTGA	5	34	1
ATGGGATGAGCGAAGGCAGTCAACGAAGAG	5	92	1
GCAGTCAACGAAGAGGCAGC          	5	107	1
          **********
MAP Score: 4.80882

Motif 2
GAAGGCAGTCAACGAAGAGGCAGC        	5	103	1
TAAACAGCAAAACGGAGACGCGTG        	3	20	1
GTTTTAAACCAGCGCCGCGGAA          	1	0	0
TTGCAGGGAGAGCGCCCCGGCACTAGACTACC	0	41	1
CTGTTTTTCTGACGTAGTGGAGAAAAA     	1	38	1
TCATTCGCGTTGCATCGAGGCGGCAACTGAGT	5	30	1
TTTGATTCATTACGCAGGAGCGTCAT      	2	159	1
ACTCAGACTAAAATAAGAGGCGGGTAGTCTAG	0	63	0
          **** ** ****
MAP Score: 4.52947

Motif 3
GTAAAGGTTGCAGGGAGAGCGCCCCGGCAC	0	34	1
CGTTTTAAACCAGCGCCGCGGAA       	1	3	0
TTTTTCAGTTCATCGAGACACCTCGCAAGT	2	73	1
GATAGATATCCAGCGAAGGATGAAGAAAAC	2	101	0
GCCTGCTAAACAGCAAAACGGAGACGCGTG	3	14	1
         ACAGGCAGGGCTATCTGGAGA	4	1	1
ATTCGCGTTGCATCGAGGCGGCAACTGAGT	5	32	1
TGAATGGGATGAGCGAAGGCAGTCAACGAA	5	89	1
          **********
MAP Score: 3.51452

Motif 4
TAGTCTAGTGCCGGGGCGCTCTCCCTGCAA	0	41	0
        TTCCGCGGCGCTGGTTTAAAAC	1	2	1
TGATTCATTACGCAGGAGCGTCAT      	2	161	1
AACAGCAAAACGGAGACGCGTG        	3	22	1
TGAGTGAACTCCCATGAGCATAGATAACTA	5	57	1
CTATGTGAATGGGATGAGCGAAGGCAGTCA	5	84	1
          **********
MAP Score: 3.23647