AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_operons038_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243628
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF0659	45	type II secretion system protein (gspE-2)
#1	AF0663	133	heterodisulfide reductase, subunit A (hdrA-1)
#2	AF0996	60	type II secretion system protein (gspE-3)
#3	AF0997	71	N-ethylammeline chlorohydrolase (trzA-2)
#4	AF1049	102	type II secretion system protein (gspE-4)

Motif 1
        ATTTGCAAGAAAAGCATATATTTTGGGAAATATAAC	0	2	1
AATCCAGGATTTTTGGAAACCGAAAACATTTTTAAGGTTAAATT	1	21	0
CTTGAAAAGAAGTTAATAAATGTATCGAAATTAAGCCACATTCG	1	66	0
 CCAGAATGCTTGCAAAAATAGGAGAAAATTTTAATTATTTCTT	2	9	1
     TGTTATGATGTTAACATAAGAAATAATTAAAATTTTCTC	2	31	0
TTTTAAGCTTTACCGCGAAAGGTATTAATCTTAAAGATTGAGGA	3	31	1
TGCAGTGTAATCCCAAAAATGAAAGCAAAGGTTAATAGCAACAT	4	25	1
CAACATCAGTTGATAGTAGTAATAGTTATTATAATGAAGGGGGG	4	63	1
          *  **  **    *   **  * *
MAP Score: 3.61163

Motif 2
 ATTTGCAAGAAAAGCATATATTTTGGGAAATATAACATTT	0	9	1
   ACTAAATAAACAATTTAACCTTAAAAATGTTTTCGGTT	1	7	1
AAATGTATCGAAATTAAGCCACATTCGAAATCCAGGATTTT	1	52	0
AAAATAGGAGAAAATTTTAATTATTTCTTATGTTAACATCA	2	24	1
         AAAATATGTTTATTTTCAGCATTTTAAGCTTT	3	1	1
CTTTACCGCGAAAGGTATTAATCTTAAAGATTGAGGACCTT	3	38	1
GTTAATAGCAACATCAGTTGATAGTAGTAATAGTTATTATA	4	55	1
          ***    *  ** **    **
MAP Score: 2.5464

Motif 3
TATTTCCCAAAATATATGCTTTTCTTGCAAAT        	0	2	0
        TGACTAAATGTTATATTTCCCAAAATATATGC	0	23	0
AATGCTTGCAAAAATAGGAGAAAATTTTAATTATTTCTTA	2	14	1
TTATGATGTTAACATAAGAAATAATTAAAATTTTCTCCTA	2	28	0
          AAAATATGTTTATTTTCAGCATTTTAAGCT	3	0	1
TAATCCCAAAAATGAAAGCAAAGGTTAATAGCAACATCAG	4	32	1
          ** *** *  *   **   *
MAP Score: 0.520939