AlignACE 3.0 10/20/99
AlignACE2 -i HI/HI_fusions005_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236353
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	HI0002	168	long chain fatty acid coA ligase, putative
#1	HI0156	300	malonyl CoA-acyl carrier protein transacylase (fabD)
#2	HI0387	300	ATP-dependent helicase (dinG)
#3	HI0389	24	outer membrane protein
#4	HI0390.1	42	long chain fatty acid coenzyme A ligase (fadD)
#5	HI1533	148	beta-ketoacyl-ACP synthase I (fabB)

Motif 1
TGAGTTTTGACCGCACTTTAAATCGGATAA	1	17	1
AAATTGGGTTCCCTTCTTTTCCACCTTTGT	1	52	1
AGAAAGGCGCCCCTACTTTTCCTTGTTTCC	1	166	0
AGTAGGGGCGCCTTTCTTTTTGCTTACTTT	1	179	1
CTTTCTTTTTGCTTACTTTTTCTTTGGCGA	1	190	1
CCGATGGCGAGCTTACTTTTTCTTTGCTTC	1	218	0
AAAATTTTTACCGCACTTTTAGCCTGACTA	2	94	1
CAAAACATAACCGTTCTTTAAAAATAGCCT	2	182	1
          **********
MAP Score: 12.9477

Motif 2
TTCGGAGCGTTTTTTATTATCTAGAATTTA	0	37	1
TTCTTCTAGCTTTTATTCCTATTTAAGATT	0	123	1
CCCAATTTGTTCTTTATCCGATTTAAAGTG	1	30	0
GGGGCGCCTTTCTTTTTGCTTACTTTTTCT	1	183	1
GAGCTTACTTTTTCTTTGCTTCGCCAAAGA	1	210	0
CTCAATAAGATTTTATTCATTTTAAAACAT	2	62	1
TGACAAATCATTTTTAACCTTTCTCATTGA	2	140	1
GCCACCAGTATTTTTATTCTTGATATTTAG	2	226	1
ATATTTAGCGTTTCTATGCGACAATCTTTG	2	248	1
          TTTCTATCCTCCAGTTATTT	3	14	0
          TTTTTATCCTAATTTGTTGG	4	32	0
         TTTTTATTCCTTTCTTGCCTA	5	1	1
CTTGAAATATTTTTATTTCGTAGTAATTTT	5	88	1
          **********
MAP Score: 12.6469

Motif 3
        TTAAAACTTTGAAAAAATTAACCGCTCTTCG	0	2	1
TTTACGCTCTAAAAATGAACAAGGGATCACTAAAAATAA	0	68	1
GGATCACTAAAAATAATTTAAAACAATCAATATTCTTCT	0	91	1
ACCGCACTTTAAATCGGATAAAGAACAAATTGGGTTCCC	1	26	1
CCTACAAATTCAATTCCACAAAGGTGGAAAAGAAGGGAA	1	60	0
AAGGCAAATTCAATGGAACAAAGGAAACAAGGAAAAGTA	1	144	1
TCGCCAAAGAAAAAGTAAGCAAAAAGAAAGGCGCCCCTA	1	181	0
ATTTTCAATTAAAAAACAATAGGACAAAACATA      	1	277	1
CTATCTATGAAAAACTCAATAAGATTTTATTCATTTTAA	2	48	1
AAGTGCGGTAAAAATTTTAGATGTTTTAAAATGAATAAA	2	73	0
TCATTGAGTAAAATCTATTCAAAACATAACCGTTCTTTA	2	163	1
      GTTTAAATAACTGGAGGATAGAAA         	3	4	1
TATTATACGCAAATTTCATTAGGCAAGAAAGGAATAAAA	5	11	0
CTACGAAATAAAAATATTTCAAGCAATAATTCATTTGTT	5	72	0
ATTTTTACATATAAAACAATAAGGAAGAAGCA       	5	126	1
          ****   *  ***    **
MAP Score: 11.8357

Motif 4
TTTGCTTCGCCAAAGAAAAAGTAAGCAAAA	1	196	0
TTTGGCGAAGCAAAGAAAAAGTAAGCTCGC	1	212	1
ATTAGGCAAGAAAGGAATAAAAA       	5	3	0
AGATGTTTTAAAATGAATAAAATCTTATTG	2	64	0
AAAAATATTTCAAGCAATAATTCATTTGTT	5	72	0
TACGCTCTAAAAATGAACAAGGGATCACTA	0	70	1
AGCAAGCTATCTATGAAAAACTCAATAAGA	2	42	1
ACAAAGGAAACAAGGAAAAGTAGGGGCGCC	1	161	1
ATAATCTTAAATAGGAATAAAAGCTAGAAG	0	125	0
TTAAATCGGATAAAGAACAAATTGGGTTCC	1	34	1
AAAGAAAAAGTAAGCAAAAAGAAAGGCGCC	1	185	0
TTTTACATATAAAACAATAAGGAAGAAGCA	5	128	1
AGGCAAATTCAATGGAACAAAGGAAACAAG	1	145	1
GAAGAATTTTCAATTAAAAAACAATAGGAC	1	272	1
    TTAAAACTTTGAAAAAATTAACCGCT	0	6	1
          **********
MAP Score: 10.6279

Motif 5
AAACTTTGAAAAAATTAACCGCTCTTCGGAGCGTT	0	13	1
 AATATTTTGAGTTTTGACCGCACTTTAAATCGGA	1	9	1
AAACATCTAAAATTTTTACCGCACTTTTAGCCTGA	2	86	1
TTTTTACCGCACTTTTAGCCTGACTAGCAAAAGAT	2	98	1
ATGACAAATCATTTTTAACCTTTCTCATTGAGTAA	2	139	1
AATCTATTCAAAACATAACCGTTCTTTAAAAATAG	2	174	1
ACCGTTCTTTAAAAATAGCCTCTATGTAATCTTAA	2	191	1
TTTATTCTTGATATTTAGCGTTTCTATGCGACAAT	2	238	1
TCTATGCGACAATCTTTGCGGTTATTTACTTTAAA	2	260	1
          *   ** **** ***
MAP Score: 9.20077

Motif 6
CCGAAGAGCGGTTAATTTTTTCAAAGTTTT	0	12	0
GTGATCCCTTGTTCATTTTTAGAGCGTAAA	0	68	0
TCTAGCTTTTATTCCTATTTAAGATTATAT	0	127	1
AACAAATTGGGTTCCCTTCTTTTCCACCTT	1	49	1
CTTTTCCTTGTTTCCTTTGTTCCATTGAAT	1	151	0
GTAGGGGCGCCTTTCTTTTTGCTTACTTTT	1	180	1
TTTCTTTTTGCTTACTTTTTCTTTGGCGAA	1	191	1
CGATGGCGAGCTTACTTTTTCTTTGCTTCG	1	217	0
ATAAGATTTTATTCATTTTAAAACATCTAA	2	66	1
GGTAATGACAAATCATTTTTAACCTTTCTC	2	135	1
     TTTTTATTCCTTTCTTGCCTAATGA	5	5	1
TCAAGCAATAATTCATTTGTTCGACCAGTT	5	63	0
     TGCTTCTTCCTTATTGTTTTATATG	5	133	0
          **********
MAP Score: 6.95924

Motif 7
GCTCCGAAGAGCGGTTAATTTTTTCAAAGTTTTAA 	0	9	0
CATTTTTAGAGCGTAAATTAAATTCTAGATAATAAA	0	49	0
TCGTCTGTTTGAGCGTAGCGAGTTCAGAAAATTTCC	1	105	1
CTCGCCATCGGCGAAACCCGATTTTAATTACCGAAG	1	237	1
AACTCAATAAGATTTTATTCATTTTAAAACATCTAA	2	60	1
CTTTCTCATTGAGTAAAATCTATTCAAAACATAACC	2	158	1
GTAATCTTAAGCCACCAGTATTTTTATTCTTGATAT	2	216	1
GACAATCTTTGCGGTTATTTACTTTAAAAATATGTT	2	267	1
ATGAATTATTGCTTGAAATATTTTTATTTCGTAGTA	5	77	1
          ***   * * * ****
MAP Score: 1.14737

Motif 8
CGCTCCGAAGAGCGGTTAATTTTTTCAAAGTTTTAA    	0	6	0
GAATTTAATTTACGCTCTAAAAATGAACAAGGGATCACTA	0	60	1
CGAACAGTTGTGCGCTAATATAATCTTAAATAGGAATAAA	0	134	0
CGATTTAAAGTGCGGTCAAAACTCAAAATATT        	1	2	0
CTGAACTCGCTACGCTCAAACAGACGAAAATTTCCTACAA	1	92	0
AGGCTAAAAGTGCGGTAAAAATTTTAGATGTTTTAAAATG	2	79	0
GTCGCATAGAAACGCTAAATATCAAGAATAAAAATACTGG	2	230	0
CGACAATCTTTGCGGTTATTTACTTTAAAAATATGTTTTA	2	266	1
          ****** **        * *
MAP Score: 0.256801