AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_fusions026_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241660
 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	AF0197	86	acetyl-CoA synthetase (acs-1)
#4	AF0568	300	A. fulgidus predicted coding region AF0568
#5	AF1261	133	medium-chain acyl-CoA ligase (alkK-4)
#6	AF1263	74	iron-sulfur cluster binding protein

Motif 1
GAGAGTGAACCATCCACAAACGAATGGGAA	0	27	1
TTCTGCTCCATCAGCCCAAAGAACCTCTCT	0	60	0
CAATAAATGAACTCATCCAAAGAATCAAAC	0	99	0
GAGGAAGCTACCTGCTGAAAGGGTGTTTGA	0	198	1
AAATAATTTCACTCCTCAAACAACCACCTC	0	234	0
TTTTCTGTGATATCCCGAAATAATTTCACT	0	251	0
        AACCTCAAGAAAAGCTTTGAAA	1	10	0
CCGAACAACAACTGACGAAATGAGCACGAT	2	37	1
AAAATTGAATTATGCTCAAAGTGTGAGCA 	3	9	0
       AGTTCACCTCCAATTTATAACAT	3	73	0
AAGCTTTCAAACTCCTCCAAAACCGAATTC	4	34	1
TAACTGGTCAACACCACAAACCTCATAAAT	4	171	0
TTTAAAGAGCAATCCAGAAAATGGG     	4	285	1
TCAGTTATAATCTGCTGAAAAACAAAAAAG	5	33	0
TTTACTTAAGAATCCTGAAAGTTTATTTTC	5	61	0
CATAGCCTTTTCTCCACAAATTATATAACA	6	44	0
          **********
MAP Score: 18.0915

Motif 2
AGAGAGGTTCTTTGGGCTGATGGAGCAGAAGCTCC	0	60	1
ATGAGCCTGAATTTTGATGAACTGGAGACTCCTTA	0	151	1
TTACCAAGCTTTTCTGAGGAAGCTACCTGCTGAAA	0	183	1
GTCAGTTGTTGTTCGGGGGAAAACGGTAACTTCCT	2	18	0
GATTTGTTTATTTATGATGATAAAGTATTTATGAA	2	64	1
AATTCAATTTTTTAAGATGATAATGAATTTAAATT	3	28	1
        ATTTTTAGCTGAACATGCTTCTTGAAG	4	2	1
CTGAATTCGGTTTTGGAGGAGTTTGAAAGCTTCAA	4	31	0
ATTAATTGGATTTATGAGGTTTGTGGTGTTGACCA	4	162	1
CTTTTTTGTTTTTCAGCAGATTATAACTGAAAATA	5	33	1
TGTTATATAATTTGTGGAGAAAAGGCTATGAGGTG	6	44	1
          ***  ******   *
MAP Score: 8.49996

Motif 3
GGAAGATAGAGAGGTTCTTTGGGCTGATGGAG	0	53	1
CTCCATCTGTTTGATTCTTTGGATGAGTTCAT	0	91	1
TTTGGATGAGTTCATTTATTGGTACAATTACG	0	108	1
AGTACGGGAGGTGGTTGTTTGAGGAGTGAAAT	0	227	1
TCAGGGCCTATTGATTAATTGGATTTATGAGG	4	149	1
TAATTTAGAATTGTGTCTTTGGTATAGGTCTC	4	233	0
TCGATTAAACTTGATTGATTGGTGAAAAACT 	5	112	1
          *** ** *****
MAP Score: 6.95833

Motif 4
AGAGAGGTTCTTTGGGCTGATGGAGCAGAAG	0	60	1
TTCATCAAAATTCAGGCTCATGTGAGGCTTA	0	141	0
CTGAGGAAGCTACCTGCTGAAAGGGTGTTTG	0	196	1
AAATAAACAAATCGTGCTCATTTCGTCAGTT	2	46	0
GATTTGTTTATTTATGATGATAAAGTATTTA	2	64	1
AAAAAATTGAATTATGCTCAAAGTGTGAGCA	3	10	0
AATTCAATTTTTTAAGATGATAATGAATTTA	3	28	1
AATGAATTTAAATTTGCTCATTAAATGTTAT	3	49	1
        ATTTTTAGCTGAACATGCTTCTT	4	2	1
TTTCAGTTATAATCTGCTGAAAAACAAAAAA	5	34	0
          *** *******
MAP Score: 4.20918

Motif 5
CTTCCCATTCGTTTGTGGATGGTTCACTCTC	0	27	0
AGAAGCTCCATCTGTTTGATTCTTTGGATGA	0	86	1
TGTTTGATTCTTTGGATGAGTTCATTTATTG	0	98	1
CCTTACCAAGCTTTTCTGAGGAAGCTACCTG	0	181	1
CTGCTGAAAGGGTGTTTGAGTACGGGAGGTG	0	209	1
ACGGGAGGTGGTTGTTTGAGGAGTGAAATTA	0	230	1
 TTTCAAAGCTTTTCTTGAGGTT        	1	9	1
ACGATTTGTTTATTTATGATGATAAAGTATT	2	62	1
GATGATAAAGTATTTATGAATACTCATACGA	2	79	1
AGCTGAACATGCTTCTTGAAGCTTTCAAACT	4	16	1
CACTGAATTCGGTTTTGGAGGAGTTTGAAAG	4	37	0
TGATTAATTGGATTTATGAGGTTTGTGGTGT	4	160	1
      CCCATTTTCTGGATTGCTCTTTAAA	4	285	0
AAACTTTCAGGATTCTTAAGTAAATTAATTC	5	67	1
          * *********
MAP Score: 2.92702

Motif 6
TTGAGGAGTGAAATTATTTCGGGATATCACA	0	245	1
ATCACAGAAAAACTTATTTTGACAAAAAGTT	0	270	1
ATTCTTAAGTAAATTAATTCGAAAAATTATT	5	78	1
TTATGATGATAAAGTATTTATGAATACTCAT	2	75	1
GAGCAAATTTAAATTCATTATCATCTTAAAA	3	37	0
TTAATTCGAAAAATTATTATGTCGATTAAAC	5	91	1
TACTCATACGAAATTATTATTCAATAAAAAA	2	99	1
TGTGAGGCTTAACGTAATTGTACCAATAAAT	0	121	0
TTCATTTTCCAACTTTTTTGTTTTTCAGCAG	5	21	1
  TACATCGTAAGTTCATTTTCCAACTTTTT	5	8	1
AGAATCCTGAAAGTTTATTTTCAGTTATAAT	5	52	0
          ********* *
MAP Score: 2.85765

Motif 7
AGACTCCTTACCAAGCTTTTCTGAGGAAGC	0	176	1
       TTTCAAAGCTTTTCTTGAGGTT 	1	3	1
      ACCACCACCCCTTTTTTATTGAAT	2	117	0
ACCCTGAATCCCGCGCCTTTGTCCGCTCGG	4	109	1
AGTTCATTTTCCAACTTTTTTGTTTTTCAG	5	19	1
GCTTTCACCTCATAGCCTTTTCTCCACAAA	6	54	0
          **********
MAP Score: 1.99441