AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_fusions020_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241594
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF0167	123	flavoprotein (fprA-1)
#1	AF0169	83	A. fulgidus predicted coding region AF0169
#2	AF0880	62	rubredoxin (rd-1)
#3	AF1348	67	A. fulgidus predicted coding region AF1348
#4	AF1520	27	flavoprotein (fprA-2)

Motif 1
TCTGCGATTCCAGTCCTTCGCACCAACCCAG	0	37	0
ATTTTTGACTCGCTCATTCCCCTCCCGCAGG	0	68	1
TAGCTGTTGTAGCTCGTTCCCTGCGGGAGGG	0	87	0
TCTCAGTTATAATCCTTTCGCTTAAATATCG	2	25	0
     CAAAAAGGTCTTTCGCTAACAGTTGT	4	5	1
          ***** *****
MAP Score: 6.07721

Motif 2
    GAGTGTGGAGATTGCTGAAAAAGTTTACTGGGTTG	0	6	1
TCTTCGGTGAAGCTTTGCGGGAAAATGGTAAAATAGTAT	1	11	0
CTTCACCGAAGATTTTAGTGGAAACTGATTTGTAGTTTC	1	38	1
TTGTTGAGGCGATATTTAAGCGAAAGGATTATAACTGAG	2	16	1
    AGGTTAGGAAATCGAGGGAAAGCTTAATATTAGAA	3	6	1
     CAAAAAGGTCTTTCGCTAACAGTTGTA       	4	5	1
          **   *   ** *** * *
MAP Score: 2.72407

Motif 3
TCGGTGAAGCTTTGCGGGAAAATGGTAAAATA	1	15	0
TCACCGAAGATTTTAGTGGAAACTGATTTGTA	1	40	1
TGAGGCGATATTTAAGCGAAAGGATTATAACT	2	20	1
AGGTTAGGAAATCGAGGGAAAGCTTAATATTA	3	10	1
GAAAGCTTAATATTAGAAAAAAGAAAAATTCG	3	27	1
    TACAACTGTTAGCGAAAGACCTTTTTG 	4	9	0
          *** ** *****
MAP Score: 2.66988

Motif 4
AGTGTGGAGATTGCTGAAAAAGTTTACTGGG	0	11	1
GTTTACTGGGTTGGTGCGAAGGACTGGAATC	0	32	1
CGGTGAAGCTTTGCGGGAAAATGGTAAAATA	1	15	0
CACCGAAGATTTTAGTGGAAACTGATTTGTA	1	41	1
 TCAATGTTGTTGAGGCGATATTTAAGCGAA	2	9	1
TGAGGCGATATTTAAGCGAAAGGATTATAAC	2	20	1
GGTTAGGAAATCGAGGGAAAGCTTAATATTA	3	11	1
    TACAACTGTTAGCGAAAGACCTTTTTG	4	10	0
          *** *******
MAP Score: 2.62134