AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID028_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943391302
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	gyrA	146	DNA gyrase, subunit A, type II topoisomerase
#1	gyrB	28	DNA gyrase subunit B, type II topoisomerase, ATPase activity
#2	dnaA	300	DNA biosynthesis; initiation of chromosome replication; can be transcription regulator

Motif 1
CCGCCTCGCGGCAGGATCGTTTACACTTAG	2	44	1
CGATCGTTTTGCAGGATCTTGACTCGGGCA	2	162	1
TGATCCGCGGTCCCGATCGTTTTGCAGGAT	2	149	1
TCACCCTCAAGCAGGGTCTTTTCGACGTAC	2	218	1
CGCGAGGCGGGCACGATTTACGCCGCATAT	2	24	0
GCTGAAACATTCATGATTGTTGACGTACGT	2	242	0
TCACAGATTTTCCCGATTTATCCACAGGAC	2	87	0
CACATCCAATGCCTGATATACTCGTTTGTC	0	36	0
          **********
MAP Score: 7.14502

Motif 2
TCTACTCCGTAATTGGCAAGACAAACGAGT	0	17	1
TTTACCTCAAACTGCGCGGCTGTGTTATAA	0	81	1
GCTGTGTTATAATTTGCGACCTTTGAATCC	0	99	1
CCCAAGTATAAATGAGCGAGAAACGTTG  	1	10	1
TAAATTTTCCAATATGCGGCGTAAATCGTG	2	13	1
GATCGTTTACACTTAGCGAGTTCTGGAAAG	2	58	1
CATAGCCTAAACTGCGCAAGAGATCTTCTG	2	121	0
          **********
MAP Score: 5.64348

Motif 3
CACTTCTACTCCGTAATTGGCAAGACAAACGA	0	13	1
TATAGGTTTACCTCAAACTGCGCGGCTGTGTT	0	75	1
TATCCCTCTACTGTATCCCGGATTCAAAGGTC	0	116	0
ACGATTTACGCCGCATATTGGAAAATTTAATG	2	10	0
AACGATCCTGCCGCGAGGCGGGCACGATTTAC	2	33	0
AGGCTATGATCCGCGGTCCCGATCGTTTTGCA	2	143	1
GGGCATATAACCGCAGACAGCGGTTCGTGCGT	2	187	1
CGTGCGTCACCCTCAAGCAGGGTCTTTTCGAC	2	212	1
          ****** * ***
MAP Score: 4.60958

Motif 4
CTCCGTAATTGGCAAGACAAACGAGTATATCAG	0	21	1
GCGCGGCTGTGTTATAATTTGCGACCTTTGAAT	0	94	1
     CCCAAGTATAAATGAGCGAGAAACGTTG	1	5	1
GCCGCATATTGGAAAATTTAATG          	2	0	0
CCGCGAGGCGGGCACGATTTACGCCGCATATTG	2	22	0
AGCGAGTTCTGGAAAGTCCTGTGGATAAATCGG	2	72	1
TGGATAAATCGGGAAAATCTGTGAGAAACAGAA	2	93	1
CGCAGTTTAGGCTATGATCCGCGGTCCCGATCG	2	135	1
          ** *****  ***
MAP Score: 0.777234