AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_fusions022_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241607
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF0042	63	polysaccharide ABC transporter, permease protein (rfbA-1)
#1	AF0968	205	3-ketoacyl-CoA thiolase (acaB-10)
#2	AF0970	101	A. fulgidus predicted coding region AF0970
#3	AF1127	213	LSU ribosomal protein L18E (rpl18E)
#4	AF1131	75	DNA-directed RNA polymerase, subunit K (rpoK)
#5	AF1132	108	enolase (eno)
#6	AF1134	74	A. fulgidus predicted coding region AF1134
#7	AF1135	99	A. fulgidus predicted coding region AF1135
#8	AF1136	103	ABC transporter, ATP-binding protein
#9	AF1843	163	cobalamin biosynthesis protein (cbiM-2)
#10	AF1845	94	conserved hypothetical protein
#11	AF1846	193	conserved hypothetical protein
#12	AF1847	50	A. fulgidus predicted coding region AF1847

Motif 1
 ATTTTTATTTTTATATTTTTGTTTTTAACA	1	9	1
TTTTTACGCGTTTAGATTTTTCATTTGCTCT	1	90	0
         ATTTAAATTTTTTCATTTATGA	2	89	0
ATTACTTTTTTTCAGATTTTTCACAAGTGCT	9	63	0
 TTACCCACCTTCACATTTTTTGTTCCTAAA	10	74	0
     GCTATTTCCCATTTTTTCTCAGCTTC	8	5	1
TTCTTTTTTATTCATAATTTTCTCCAAAATA	9	12	1
CATTACGTAATTTAAATCTTTGCCGCATGTT	3	59	0
GCGGGTTTGTTTTACATTCTTAGCATAGCG 	9	143	1
GCGAAGCTGATTAAAAATTTTGCTCTAAGTT	0	21	1
TACTTGATATATTCAATTTTTACGCGTTTAG	1	106	0
ACAGGCGGATTATCTATTTTTAAATCGGCAC	1	157	1
       ATCTTATAATTTTTCCCTTAAGCT	11	179	0
CTAAGATAATTATATAATTTTCTACAAATTA	6	41	0
AGTTTTTGATTTTAGTATTTTGGAGAAAATT	9	27	0
TTAATTCGAAATCAAAATTTTCTTATAAGGG	10	35	1
          TTTTCTTTTTTATTCATAATT	9	0	1
CTTTGCCGCATGTTAATTTTTAATGTTCCTT	3	42	0
          **** ******
MAP Score: 15.2281

Motif 2
TAAAAACAGCGTGTTAAAAACAAAAATATAAAAATA	1	15	0
AAATCTAAACGCGTAAAAATTGAATATATCAAGTAT	1	102	1
CAAATTAATGGTGATAATTAGGATAACAAAAAATAA	6	12	0
TTAGGAAGCTGAGAAAAAATGGGAAATAGC      	8	4	0
TAGTATTTTGGAGAAAATTATGAATAAAAAAGAAAA	9	10	0
ATTAGCACTTGTGAAAAATCTGAAAAAAAGTAATAC	9	60	1
TTACAGGGAGGAGGAAATCCTGAAAATTGCCCTCGA	11	11	1
TTCCCGAAAAGGGTAAAGCTCGAACAGCTTGCAGAG	11	63	1
GAAAGCTTAAGGGAAAAATTATAAGAT         	11	176	1
GGGCTGCTGAGGGTAAAGGGAGAAAACGCTTGGGAG	12	12	1
          * *****    *** *
MAP Score: 15.0916

Motif 3
CCTTCACATTTTTTGTTCCTAAACTGTGCATC	10	65	0
TCAACATTAGTTGTGTTCATAAATGAAAAAAT	2	73	1
AGCTTCCTAATTGTCATCATAATGTATTTACC	8	30	1
 GTTTATTTTTTGTTATCCTAATTATCACCAT	6	9	1
ATTTTTATATTTTTGTTTTTAACACGCTGTTT	1	16	1
AGCAAATGACTTTTGCTTATAAAATTGTTCCG	7	68	0
 ATCTTATAATTTTTCCCTTAAGCTTTCCCGA	11	172	0
CTCAGCGTAGTTTTGACCGTTACATTACGTAA	3	80	0
TTGTTCCGTGTTGTCGTCTTTACCTAAGGGAA	7	44	0
CTAATAAAGTTTTTGATTTTAGTATTTTGGAG	9	33	0
AAATGGGTTGTTTTTCCCTTAGGTAAAGACGA	7	31	1
TGATTAAAAATTTTGCTCTAAGTTTAAAAACA	0	28	1
          TTTTCTTTTTTATTCATAATTT	9	0	1
TTATTCATAATTTTCTCCAAAATACTAAAATC	9	19	1
CTTGCAGAGTTTTTCGGCATAGCCCCCTCGAC	11	90	1
         ATTTTTATTTTTATATTTTTGTT	1	1	1
GATTTTTCATTTGCTCTCGTAATTAATTATTG	1	75	0
TCCCAAGCGTTTTCTCCCTTTACCCTCAGCAG	12	15	0
ATCCTGAAAATTGCCCTCGAAAAGGGATACTT	11	27	1
          ***** ** ***
MAP Score: 11.433

Motif 4
TGAGCTCAATGTTTTTAAACTTAGAGCAAAA	0	38	0
TTATATTTTTGTTTTTAACACGCTGTTTTTA	1	20	1
TTAACACGCTGTTTTTAGCGTACTGTATTTA	1	34	1
TTAGCGTACTGTATTTAGCTTTAATGTCAAT	1	48	1
TATCGAAATCGTTTTTAGCCTTCCGCGGAAG	3	14	1
CCTCAGCGTAGTTTTGACCGTTACATTACGT	3	82	0
          CTTTTTAACTTACCTTACGCC	7	0	1
CAAATGGGTTGTTTTTCCCTTAGGTAAAGAC	7	30	1
         GCTATTTCCCATTTTTTCTCAG	8	1	1
TCATCATAATGTATTTACCATATCACATCTC	8	43	1
  ATCTTATAATTTTTCCCTTAAGCTTTCCC	11	174	0
          ********* *
MAP Score: 9.80431

Motif 5
TGATATTTAAAATGAGTGTATCTGCAAAAGCTTTATAT	2	34	0
TCAAAACTACGCTGAGGTGTAGTTGATATGAGCAAGAT	3	96	1
AAGGAAGCTGGCAGAGGAGGAAGTCAAATCCAAACCTC	3	134	1
TCGATGTACTGCTGAGCGAGTCAGCAAAAAATGAGGCG	3	182	1
GACGTTCACTACAGAGTCGTTTTCGACAGCAGGGGAAA	5	31	1
CAATTAGGAAGCTGAGAAAAAATGGGAAATAGC     	8	5	0
AAAGTAATACGAGGTGAGAAATTGCACATCCCTGATGG	9	86	1
  CTTACAGGGAGGAGGAAATCCTGAAAATTGCCCTCG	11	8	1
CGAACAGCTTGCAGAGTTTTTCGGCATAGCCCCCTCGA	11	83	1
AAAGGTGCTGGAGAAGTACTTCGGGAAAGCTTAAGGGA	11	152	1
   AGGGGCTGCTGAGGGTAAAGGGAGAAAACGCTTGG	12	7	1
          ** ***    *  *** *
MAP Score: 9.66226

Motif 6
TTAGCCTTCCGCGGAAGGAACATTAAAAATTAACATGC	3	28	1
TCAAAACTACGCTGAGGTGTAGTTGATATGAGCAAGAT	3	96	1
ATATGAGCAAGATAAGGAAGCTGGCAGAGGAGGAAGTC	3	121	1
GCTGGCAGAGGAGGAAGTCAAATCCAAACCTCGTTACT	3	140	1
TCGATGTACTGCTGAGCGAGTCAGCAAAAAATGAGGCG	3	182	1
CTTGATAATTGAGGACGTTCACTACAGAGTCGTTTTCG	5	18	1
AGTCGTTGCTGGGGAGGTTGTTGCGAAGGCG       	5	87	1
AACCCATTTGGCGTAAGGTAAGTTAAAAAG        	7	2	0
TGATGACAATTAGGAAGCTGAGAAAAAATGGGAAATAG	8	11	0
  CTTACAGGGAGGAGGAAATCCTGAAAATTGCCCTCG	11	8	1
TGATAGAGTCGAGGGGGCTATGCCGAAAAACTCTGCAA	11	91	0
GAAGTACTTCGGGAAAGCTTAAGGGAAAAATTATAAGA	11	164	1
   AGGGGCTGCTGAGGGTAAAGGGAGAAAACGCTTGG	12	7	1
AGAAAACGCTTGGGAGGTGTTAGAGAAA          	12	32	1
          * *****       ****
MAP Score: 8.91062

Motif 7
TGAAGTCGTTGCTGGGGAGGTTGTTGCGAA	5	84	1
AAGGAAGCTGGCAGAGGAGGAAGTCAAATC	3	134	1
GGGAGAAAACGCTTGGGAGGTGTTAGAGAA	12	29	1
ACCCCTTAAAGCAGATGGGGCCGCCGAGAT	4	54	0
      AGGGGCTGCTGAGGGTAAAGGGAG	12	4	1
TCGATGTACTGCTGAGCGAGTCAGCAAAAA	3	182	1
CTCGATTTGAGCATAGCGGGTTTGTTTTAC	9	128	1
    GCTGGAGCTTGGTAGGGGAGAATATA	8	87	0
CTCTGATAGAGTCGAGGGGGCTATGCCGAA	11	102	0
AGAAAAAGGTGCTGGAGAAGTACTTCGGGA	11	148	1
GTTTTCGACAGCAGGGGAAACGAGACGGTT	5	49	1
          **********
MAP Score: 7.884

Motif 8
AATTTTTAATCAGCTTCGCTAAGGCAGGCT 	0	9	0
CCTCCTCTGCCAGCTTCCTTATCTTGCTCAT	3	123	0
ACTCGGGTCACGGCGTCCCGAACGCCGCAGG	4	19	0
GTTCAAATCTCGGCGGCCCCATCTGCTTTAA	4	48	1
GCCTTCGCAACAACCTCCCCAGCAACGACTT	5	86	0
          CGCCTTCGCAACAACCTCCCC	5	97	0
CATTTTTTCTCAGCTTCCTAATTGTCATCAT	8	19	1
AGGGATACTTCGATTTCCCGAAAAGGGTAAA	11	49	1
          ********* *
MAP Score: 6.19049

Motif 9
GAGCTCAATGTTTTTAAACTTAGAGCAAAATT	0	36	0
         ATTTTTATTTTTATATTTTTGTT	1	1	1
TATTTTTATATTTTTGTTTTTAACACGCTGTT	1	15	1
TGTACCGAATTTGTTCCAATTAATACTTGATA	1	128	0
          TTTTTATAATTAACAAATCTGG	2	0	1
   ATTTAAATTTTTTCATTTATGAACACAAC	2	82	0
       GTTTATTTTTTGTTATCCTAATTAT	6	3	1
TTTGTAGAAAATTATATAATTATCTTAGGTTA	6	44	1
          CTTTTTAACTTACCTTACGCCA	7	0	1
          TTTTCTTTTTTATTCATAATTT	9	0	1
GCTAATAAAGTTTTTGATTTTAGTATTTTGGA	9	34	0
GCGGGTTTGTTTTACATTCTTAGCATAGCG  	9	143	1
ACCTTCACATTTTTTGTTCCTAAACTGTGCAT	10	66	0
          ***** ** ***
MAP Score: 3.65324

Motif 10
ATTATTGACATTAAAGCTAAATACAGTACGC	1	51	0
ATTGAATATATCAAGTATTAATTGGAACAAA	1	120	1
TACGTAAAATTTAAGTATTAACGAA      	1	190	1
GCCAGATTTGTTAATTATAAAAA        	2	2	0
TACACTCATTTTAAATATCAATCAACATTAG	2	52	1
TTGCCGCATGTTAATTTTTAATGTTCCTTCC	3	40	0
GTGAACGTCCTCAATTATCAAGCTACCACC 	5	9	0
GATTTCGAATTAAAATATCAAACGAATTGAT	10	17	0
          **** ******
MAP Score: 0.922268