AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_fusions016_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241492
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF0680	145	glutamine ABC transporter, ATP-binding protein (glnQ)
#1	AF1019	30	conserved hypothetical protein
#2	AF1020	57	A. fulgidus predicted coding region AF1020
#3	AF1468	231	A. fulgidus predicted coding region AF1468
#4	AF1817	139	transcriptional regulatory protein, TetR family

Motif 1
      ATTTGAATTTTTGTCGTTCAACTAT	2	42	0
         AGCATTTTGGTTCAAACAATTC	3	1	1
TTGGTTCAAACAATTCTGGTCTGTGCGGTTA	3	16	1
AGCAACTTGGAAATTCTCGTCAGAGAAGCTC	3	56	0
CAGATAAAATCCTTTATTGTTTTCATCTATA	3	128	1
GAAAGATGTGCATTTTTGGTCCATTTTTCCA	3	171	0
AGCAGGTTTCCCTTTATGGTTTCATCTCTGG	4	19	0
    AAGGTTACTTTGTAGTCAGAAATTTAA	4	122	0
          ***** *****
MAP Score: 6.26334

Motif 2
   TACACCACCTTGTTTAACTCTATTAATC	0	7	1
CTATTAATCCCTCTATATAAACATTATACTA	0	29	1
TAACTGTTGCCTCTCTTTAAAATTCACTTCG	0	58	1
TTATATAAAATCTTTTTTCTCGTGCGTACTA	0	105	0
AGAAAAAAGATTTTATATAACAAACCTAAAC	0	116	1
CTGCGATGGCTTCTTGTTATC          	1	19	1
          CTTTGTATCTCAACTTGAGGA	2	0	1
      AGCATTTTGGTTCAAACAATTCTGG	3	4	1
TTCCAAGTTGCTCCTTTTCTCAGACTTCCGA	3	75	1
AAATGCACATCTTTCTTTCTCCCAGGTTATA	3	187	1
GGGAAACCTGCTTTTTATCTCCGCTATTATA	4	38	1
CAGTGATTTATTTCGGATATCACACGACCGA	4	76	1
          **** ******
MAP Score: 5.23517

Motif 3
AACTATTAAACTTTATATCCTCAAGTTGAGATACAAAG      	2	4	0
CCAAGTTGCTCCTTTTCTCAGACTTCCGACAACCACAACCTTCG	3	77	1
ACAACCACAACCTTCGCCCTTTGCAGATAAAATCCTTTATTGTT	3	105	1
AAATGCACATCTTTCTTTCTCCCAGGTTATATACTCCCCGCTGC	3	187	1
GGGAAACCTGCTTTTTATCTCCGCTATTATACCCAGCACAGTGA	4	38	1
CAGCACAGTGATTTATTTCGGATATCACACGACCGATTTTAATG	4	71	1
          **** * **         * *  *
MAP Score: 1.41582