AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_fusions017_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241533
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF0194	300	A. fulgidus predicted coding region AF0194
#1	AF0195	22	A. fulgidus predicted coding region AF0195
#2	AF0196	131	medium-chain acyl-CoA ligase (alkK-1)
#3	AF0262	189	medium-chain acyl-CoA ligase (alkK-2)
#4	AF0366	218	acetyl-CoA synthetase (acs-2)
#5	AF1287	300	acetyl-CoA synthetase (acs-6)
#6	AF1928	142	tungsten formylmethanofuran dehydrogenase, subunit D (fwdD-2)
#7	AF1932	84	long-chain-fatty-acid--CoA ligase (fadD-8)

Motif 1
GTAAGGCACATTCTTGCGAGAGTGAACCAT	0	10	1
TGTTTGATTCTTTGGATGAGTTCATTTATT	0	98	1
TGAGCCTGAATTTTGATGAACTGGAGACTC	0	152	1
TACCAAGCTTTTCTGAGGAAGCTACCTGCT	0	184	1
GAAAAACTTATTTTGACAAAAAGTTAAAGT	0	276	1
TCAGTTGTTGTTCGGGGGAAAACGGTAACT	2	22	0
GAATAATAATTTCGTATGAGTATTCATAAA	2	91	0
TTGTCGCCGGTTTTTGTGAACCTTTTCAAT	3	11	0
AAAATGAAAATTTTTGCGAAAATTAAAACA	4	109	0
TTTAACCTATTTTTGGTGATGAATAGATGA	4	175	1
TCCAGCGCGCTTTTGGCAAAGTTTAA    	6	6	0
CCGTTCTCTTTTTGGGCGAGGAGAAAAATA	6	76	0
CACCAAAAGTTTTTGAGGAAGTCTTAACAA	6	117	0
CCTCAAAAACTTTTGGTGATAGG       	6	129	1
          **********
MAP Score: 12.945

Motif 2
AGACTCCTTACCAAGCTTTTCTGAGGAAGCT	0	176	1
TGACAAAAAGTTAAAGTTTTC          	0	289	1
       TTTCAAAGCTTTTCTTGAGGTT  	1	3	1
CCGGTTTTTGTGAACCTTTTCAATT      	3	4	0
GTATAGAAATTTAAGCTTTGCCCTCAGAAGC	3	133	1
TTAATTTTCGCAAAAATTTTCATTTTTAATC	4	113	1
GGATAGTGTCTCGAACTTTTCTTCTCTCTGC	5	91	1
TCTGAAAACTTAAAACTTTTCATTTAATTCA	5	210	1
          TTAAACTTTGCCAAAAGCGCG	6	0	1
TAGTGTTTATTAAAAGTTTTTTTTATATATC	6	34	0
  CCTATCACCAAAAGTTTTTGAGGAAGTCT	6	123	0
          * *********
MAP Score: 12.5335

Motif 3
GATGGTTCACTCTCGCAAGAATGTGCCTTAC	0	10	0
AGCAGGTAGCTTCCTCAGAAAAGCTTGGTAA	0	183	0
TATTTCGGGATATCACAGAAAAACTTATTTT	0	259	1
AAAAACTTATTTTGACAAAAAGTTAAAGTTT	0	277	1
AATTGAAAAGGTTCACAAAAACCGGCGACAA	3	10	1
TTTAAGCTTTGCCCTCAGAAGCAACAATCTT	3	142	1
GTGAGCAAATTTGCGCAAAAGTGTTTTAATT	4	88	1
GTGTTTTAATTTTCGCAAAAATTTTCATTTT	4	108	1
ATAGCCGATGTCTCTCACAAAGTCTATGTGT	5	19	1
    TTAAACTTTGCCAAAAGCGCGCTGGAT	6	6	1
ATTTTTCTCCTCGCCCAAAAAGAGAACGGTT	6	77	1
TTGTTAAGACTTCCTCAAAAACTTTTGGTGA	6	117	1
          **** ******
MAP Score: 9.55871

Motif 4
GACTCCTTACCAAGCTTTTCTGAGGAAGCTACC	0	177	1
CTACCTGCTGAAAGGGTGTTTGAGTACGGGAGG	0	205	1
      TTTCAAAGCTTTTCTTGAGGTT     	1	4	1
TTATGATGATAAAGTATTTATGAATACTCATAC	2	75	1
CATTGAACACATAGACTTTGTGAGAGACATCGG	5	23	0
ATTGAAGTTAATACAGTTTATGATCCAACGGAC	5	55	0
CATCTTTTACATAGTATTTAAGAATTTTGATTC	5	245	0
GTGTTTATTAAAAGTTTTTTTTATATATCCAGC	6	30	0
GAGAAAAATAATAGTCTTTCGTAGTGTTTATTA	6	53	0
GAACGGTTAAATAGTATTTGTTAAGACTTCCTC	6	100	1
CCTATCACCAAAAGTTTTTGAGGAAGTCTTAAC	6	119	0
          ****  *** ***
MAP Score: 8.89193

Motif 5
GTGATATCCCGAAATAATTTCACTCCTCAAACAACCA	0	238	0
CTTATTTTGACAAAAAGTTAAAGTTTTC         	0	282	1
TTGTTCGGGGGAAAACGGTAACTTCCTGTTTTCCC  	2	8	0
GCTTCTGAGGGCAAAGCTTAAATTTCTATACCGACAA	3	127	0
CCCTCAGAAGCAACAATCTTAAATAATTGTTTAGTAA	3	153	1
TTCGATGGTACAACAAGGTACATTGTTGTGCACTGCA	4	43	1
TTAATTTTCGCAAAAATTTTCATTTTTAATCGTTAAT	4	113	1
AGTTAAATATCAATAATTTAACCTATTTTTGGTGATG	4	159	1
TGAATTAAATGAAAAGTTTTAAGTTTTCAGAACAATG	5	204	0
CAATTCGAATCAAAATTCTTAAATACTATGTAAAAGA	5	239	1
CGCCCAAAAAGAGAACGGTTAAATAGTATTTGTTAAG	6	88	1
AAAAGCTCATGATAAACCTTAAATAATTCCAGAAACA	7	49	1
          *** *   **** *  *
MAP Score: 6.28688

Motif 6
GAGAGGTTCTTTGGGCTGATGGAGCAGAAGCTCC	0	61	1
CTACCTGCTGAAAGGGTGTTTGAGTACGGGAGGT	0	205	1
GGTGTTTGAGTACGGGAGGTGGTTGTTTGAGGAG	0	219	1
TTATTCAATAAAAAAGGGGTGGTGGT        	2	115	1
CTATACCGACAAGGAGAGCAAGAGCCGCCGTAGC	3	105	0
CTATGTGTTCAATGTCCGTTGGATCATAAACTGT	5	42	1
TATTAACTTCAATGCCGGATAGTGTCTCGAACTT	5	75	1
AGCTTTTTGCAACCACGGTTTGAGACATTTCTCT	5	124	1
AAAATGTAGGTAAGGGAGGTTGTT          	5	286	1
AACTTTGCCAAAAGCGCGCTGGATATATAAAAAA	6	13	1
          ** * * * *****
MAP Score: 1.61184