AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID028_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943391156
 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
CACATCCAATGCCTGATATACTCGTTTGTC	0	36	0
CACGATTTACGCCGCATATTGGAAAATTTA	2	13	0
CGCGAGGCGGGCACGATTTACGCCGCATAT	2	24	0
CCGCCTCGCGGCAGGATCGTTTACACTTAG	2	44	1
TCACAGATTTTCCCGATTTATCCACAGGAC	2	87	0
TGATCCGCGGTCCCGATCGTTTTGCAGGAT	2	149	1
CGATCGTTTTGCAGGATCTTGACTCGGGCA	2	162	1
TCACCCTCAAGCAGGGTCTTTTCGACGTAC	2	218	1
GCTGAAACATTCATGATTGTTGACGTACGT	2	242	0
          **********
MAP Score: 7.63858

Motif 2
GTATAGGTTTACCTCAAACTGCGCGGCTGTGTT	0	74	1
ATTAAATTTTCCAATATGCGGCGTAAATCGTGC	2	11	1
TAAGTGTAAACGATCCTGCCGCGAGGCGGGCAC	2	40	0
CGCGGATCATAGCCTAAACTGCGCAAGAGATCT	2	125	0
CGGGCATATAACCGCAGACAGCGGTTCGTGCGT	2	186	1
TCGTGCGTCACCCTCAAGCAGGGTCTTTTCGAC	2	211	1
          *** ** ** ***
MAP Score: 6.18568

Motif 3
TTCTACTCCGTAATTGGCAAGACAAACGAGT	0	16	1
GTTTACCTCAAACTGCGCGGCTGTGTTATAA	0	80	1
GGCTGTGTTATAATTTGCGACCTTTGAATCC	0	98	1
 CCCAAGTATAAATGAGCGAGAAACGTTG  	1	9	1
TTAAATTTTCCAATATGCGGCGTAAATCGTG	2	12	1
GGATCGTTTACACTTAGCGAGTTCTGGAAAG	2	57	1
TAAATCGGGAAAATCTGTGAGAAACAGAAGA	2	97	1
TCATAGCCTAAACTGCGCAAGAGATCTTCTG	2	121	0
          ***** *****
MAP Score: 5.0713

Motif 4
TGGCAAGACAAACGAGTATATCAGGCATTG	0	30	1
GGATGTGAATAAAGCGTATAGGTTTACCTC	0	59	1
CAGTAGAGGGATAGCGGTTAG         	0	135	1
TCTGTTTCTCACAGATTTTCCCGATTTATC	2	95	0
TCTGTGAGAAACAGAAGATCTCTTGCGCAG	2	110	1
AACGATCGGGACCGCGGATCATAGCCTAAA	2	140	0
ATAACCGCAGACAGCGGTTCGTGCGTCACC	2	193	1
          **********
MAP Score: 2.75292

Motif 5
 TGGCACTTCTACTCCGTAATTGGCAAGACAAACGA	0	9	1
AGCGTATAGGTTTACCTCAAACTGCGCGGCTGTGTT	0	71	1
CCGCTATCCCTCTACTGTATCCCGGATTCAAAGGTC	0	116	0
GGGCACGATTTACGCCGCATATTGGAAAATTTAATG	2	10	0
GCGGCGTAAATCGTGCCCGCCTCGCGGCAGGATCGT	2	28	1
ACAGAAGATCTCTTGCGCAGTTTAGGCTATGATCCG	2	120	1
GTTTAGGCTATGATCCGCGGTCCCGATCGTTTTGCA	2	139	1
ACTCGGGCATATAACCGCAGACAGCGGTTCGTGCGT	2	183	1
GGTTCGTGCGTCACCCTCAAGCAGGGTCTTTTCGAC	2	208	1
          *   *****  * ***
MAP Score: 1.87852