AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID017_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943391041
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	nadC	87	quinolinate phosphoribosyltransferase
#1	nadA	300	quinolinate synthetase, A protein
#2	nadB	300	quinolinate synthetase, B protein

Motif 1
AGGCGCTTTTTTGCTATTCAGGCATCCTCAATTT	1	53	1
TCGTCAGAGCTTACTGTGCAAGCAACTCTATGTC	1	108	1
TCGGTGTAATTTGTTTTATATGCTAAACAAGATA	1	215	0
 CTTACCATCTCGTTTTACAGGCTTAACGTTAAA	1	277	0
GCATCTGTTTTTGTTTGTCATGCTGTAGACGGAT	2	18	1
GGCCGTTGGGTTACTCTTCAGGCAGTTAAATGGG	2	110	0
TTTGTTACAGTTGCTAAACACGCTGACGCAGGGC	2	198	0
TTTGTTTAATTTACTAAACATGGTTTGGTCAGCA	2	272	0
          *****   ** ***
MAP Score: 13.8347

Motif 2
GGTGCTAATACCCGGTTCAGAGTAGCATGTTTCT	0	29	1
ACGCCTAATTCCACCGACATAGAGTTGCTTGCAC	1	123	0
ACAAATTACACCGATAACAGCGAATATTACGCTA	1	235	1
AACGTTAAAACCGACATTAGCGTAATATTCGCTG	1	252	0
AGATAATGATCCGTCTACAGCATGACAAACAAAA	2	26	0
ACCACCTAATCCTCCACCAGCCAGTAACTTCTCT	2	154	1
TTCTCGCCGCCCTGCGTCAGCGTGTTTAGCAACT	2	190	1
          **  *  *******
MAP Score: 5.49108

Motif 3
      CGAGTCATCCTGCACGACCCACCA	1	4	1
TGCTATTCAGGCATCCTCAATTTCACTTTG	1	64	1
GTAAAATGACGCATCCTGCACATTAGGCGT	1	155	1
GTTTTAACGTTAAGCCTGTAAAACGAGATG	1	275	1
TTTTTGTTTGTCATGCTGTAGACGGATCAT	2	25	1
TTTCACCACCTAATCCTCCACCAGCCAGTA	2	150	1
          **********
MAP Score: 5.03459

Motif 4
TGGTGCTAATACCCGGTTCAGAGTAGCATGTTTCTACC	0	28	1
GGTTCAGAGTAGCATGTTTCTACCTTATGATTCGTTAG	0	42	1
TGACGATGTCATCAGGTTTACAAAGTGAAATTGAGGAT	1	76	0
CCATTCGACTATCTTGTTTAGCATATAAAACAAATTAC	1	206	1
TCCGTAACGCATCTGTTTTTGTTTGTCATGCTGTAGAC	2	10	1
GCCCTGCGTCAGCGTGTTTAGCAACTGTAACAAATATT	2	198	1
TCAGCATAGCATCATGTTGTGCGGATAAACACCTGCTA	2	240	0
TGCTGACCAAACCATGTTTAGTAAATTAAACAAAGAAA	2	272	1
          * * ***** *    * *
MAP Score: 4.81056

Motif 5
CCGGTTCAGAGTAGCATGTTTCTACCTTAT	0	40	1
      CGAGTCATCCTGCACGACCCACCA	1	4	1
TCTGACGATGTCATCAGGTTTACAAAGTGA	1	86	0
GTAAAATGACGCATCCTGCACATTAGGCGT	1	155	1
GTTTTAACGTTAAGCCTGTAAAACGAGATG	1	275	1
TTTTTGTTTGTCATGCTGTAGACGGATCAT	2	25	1
GGGTTACTCTTCAGGCAGTTAAATGGGCAT	2	107	0
TAATCCTCCACCAGCCAGTAACTTCTCTTT	2	160	1
CCGCCCTGCGTCAGCGTGTTTAGCAACTGT	2	196	1
GGTCAGCATAGCATCATGTTGTGCGGATAA	2	250	0
          **********
MAP Score: 4.60666