AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID005_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943390917
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	glnK	180	nitrogen regulatory protein P-II 2
#1	amtB	29	probable ammonium transporter
#2	glnB	60	regulatory protein P-II for glutamine synthetase
#3	yfhG	164	putative alpha helix protein

Motif 1
TGCAAAAATGTAACGCACTGTGCACTGTCATAG	0	33	1
GTTTTTCATTTCTGGCACACCGCTTGCAATACC	0	110	1
        TCTCTGGCACACAGCAACAGGAACG	1	2	1
TATTTGTCAGTTCGGCCCCGGGCAGTGCTCGAA	3	39	1
TCTGCAACAATTACGCCCACTGGGATAGGCTTT	3	128	1
          *  ******* **
MAP Score: 5.29013

Motif 2
ATAGCGCAATATTTCATCGTTGGTGCAAAAATG	0	10	1
TCTTTCTCGTTTTTCATTTCTGGCACACCGCTT	0	102	1
          AGATCCCCTCCGGTCAGAATTCG	0	167	0
          TTTTCGTTCCTGTTGCTGTGTGC	1	16	0
TTTATTTGTCAGTTCGGCCCCGGGCAGTGCTCG	3	37	1
CACGTACGATATGTACGCTCCGGTTTCTCCGCG	3	77	1
ACGCTCCGGTTTCTCCGCGCTGTCCATGTCCAG	3	91	1
CGCGCTGTCCATGTCCAGACTGTCTGCAACAAT	3	106	1
TCTGCAACAATTACGCCCACTGGGATAGGCTTT	3	128	1
          ** *** * ****
MAP Score: 3.85401

Motif 3
AAAAATGTAACGCACTGTGCACTGTCATAGTGC	0	36	1
AGGTATTGCAAGCGGTGTGCCAGAAATGAAAAA	0	111	0
GAACCATTACCGAATTCTGACCGGAGGGGATCT	0	157	1
TCGTTCCTGTTGCTGTGTGCCAGAGA       	1	3	0
AGTTCGGCCCCGGGCAGTGCTCGAAATCTTCAC	3	47	1
TCTTCACGTACGATATGTACGCTCCGGTTTCTC	3	73	1
ATGTACGCTCCGGTTTCTCCGCGCTGTCCATGT	3	87	1
GCAACAATTACGCCCACTGGGATAGGCTTTAAG	3	131	1
          ***  ***** **
MAP Score: 2.15696

Motif 4
CAAAAATGTAACGCACTGTGCACTGTCATAG	0	35	1
GAAAATGAAAACGCACTATGACAGTGCACAG	0	50	0
 AGATCCCCTCCGGTCAGAATTCGGTAATGG	0	160	0
     TGCTAACAGCCTATCCTATCAGGCTA	3	5	1
CTGCCCGGGGCCGAACTGACAAATAAAATAG	3	33	0
CAGTTCGGCCCCGGGCAGTGCTCGAAATCTT	3	46	1
CGCGGAGAAACCGGAGCGTACATATCGTACG	3	79	0
TCCGGTTTCTCCGCGCTGTCCATGTCCAGAC	3	95	1
CTGTCCATGTCCAGACTGTCTGCAACAATTA	3	110	1
TGCAACAATTACGCCCACTGGGATAGGCTTT	3	130	1
          **** ******
MAP Score: 1.19731