AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_operons019_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243061
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF0932	41	conserved hypothetical protein
#1	AF0933	22	branched-chain amino acid aminotransferase (ilvE)
#2	AF1192	50	conserved hypothetical protein
#3	AF1195	27	activator 1, replication factor C, 53 KD subunit
#4	AF1196	65	N5,N10-methylenetetrahydromethanopterin reductase (mer-2)
#5	AF1197	300	3-ketoacyl-CoA thiolase (fadA-2)
#6	AF1211	108	conserved hypothetical protein
#7	AF1512	71	conserved hypothetical protein
#8	AF1513	257	A. fulgidus predicted coding region AF1513
#9	AF1514	199	A. fulgidus predicted coding region AF1514
#10	AF1540	143	succinyl-CoA synthetase, beta subunit (sucC-1)
#11	AF1542	135	conserved hypothetical protein
#12	AF1938	112	conserved hypothetical protein
#13	AF2186	65	succinyl-CoA synthetase, beta subunit (sucC-2)
#14	AF2187	174	A. fulgidus predicted coding region AF2187

Motif 1
TGAGAAATCTCCCTGTTGGCT          	4	54	1
    ACAACTCCCGGATACCTCGACGGTAGC	5	6	1
GGCCCCTACAGGGTGATAACGCAGATTGGTG	5	67	1
AAGGACGTAACGTTGAGGACGTGTTGAATAA	5	149	1
AAATTATCATCCCGGAGGAAGTCGAGTACAC	5	191	1
GGCGTTAGGCCGGGGTTGCCGAGCGGTAAGG	8	28	1
CGCCTGGAGAGCGTGTGGGCGTTCGCCCGCG	8	63	1
CAACAGCGCCGGGGGTGGGATTCGAACCCAC	8	93	0
CCACCCCCGGCGCTGTTGTATCTTGGCTGTT	8	106	1
GTTGTATCTTGGCTGTTGAATCTTACCGGAA	8	120	1
GAACTTAAAAGGTGGTTGGATGTGCAGGCAG	10	81	1
CCGCCGCTAAGGCTGATGACGCCTGTTCTCA	11	23	0
CAGCCTTAGCGGCGGTTGAAGGTGGACGCCA	11	39	1
GAATCGGTATGGGTGATGGCGTCCACCTTCA	11	55	0
      GAAGGCTGGTGGAATTAGGGATTTA	12	97	0
TGCTATATCTGGCTGATATAGCCTTTTCTCG	14	126	0
          ******** **
MAP Score: 12.1109

Motif 2
   TTTTAATTTTTATTTTTTCCAACAGATAGTTA	4	7	1
CTCCTTCACTTTTTTCTTATTAAAATACCATCCGG	5	268	0
ACAGATAGGATTTAACTTATTATATTTGATTAATC	6	13	1
AACGGCAGATTTTTCTCTCTTAAATACCTTTTTTA	6	78	0
AGTTTTTATGCTTGCTTTTTTGGAAATTCCACAGA	8	158	0
TATGTTCGACTGTTTGTTTTTATAAAGCTTTTTAT	9	16	1
TACTGTGGAGTTTATACTTTTAAAAAAAGGCGTTT	9	87	0
TCTTAAGCGATTTCCGGTTTTCAAACTTATAAAAG	9	142	1
TAAAAGCCTTTTTCCGCTTTTATAAGTTTGAAAAC	9	158	0
GGAAAAAGGCTTTTATATATTATAAGCCAAA    	9	178	1
  GTTACTATTTAAATTTTTTGGAAAAGAAATTCC	10	8	1
ATTCCGAAAATTTTTTATATTGAAAAATTGAGAAT	10	38	1
TACAAAAAATTTAATTATTTTAAAAATAAGACATT	12	14	0
ATTGATTTGTCTTTGAGTCTTGTAACGGTTTTTCT	14	49	0
          ***    ***** **
MAP Score: 8.9872

Motif 3
ATTTAAAACGTTTTTCCGTT          	0	0	0
TTCACCCTTCATTTCTGGTTG         	1	11	1
CAACAGGGAGATTTCTCATTACTTATACTT	4	42	0
CCTCCTTCACTTTTTTCTTATTAAAATACC	5	274	0
AACGGCAGATTTTTCTCTCTTAAATACCTT	6	83	0
         CTTTTTTCGAATTATTTTCTA	7	1	1
ACAGAAGTAATTTTCCGGTAAGATTCAACA	8	133	0
TTATGCTTGCTTTTTTGGAAATTCCACAGA	8	158	0
TTTTCCTTTCTTTTTTGATTGATTATTATA	8	206	0
        GAATTTCCCGATAAATAATTAC	8	245	0
TTTGGGGATTATTTCTCGCTAAAAACGCCT	9	65	1
TTCTTAAGCGATTTCCGGTTTTCAAACTTA	9	141	1
TATAAAAGCCTTTTTCCGCTTTTATAAGTT	9	165	0
ACTATTTAAATTTTTTGGAAAAGAAATTCC	10	13	1
AATATAAAAAATTTTCGGAATTTCTTTTCC	10	29	0
AACATTCTCAATTTTTCAATATAAAAAATT	10	46	0
      ATCGATTTTCGATATCGGTTCTCG	11	121	0
AATAATTAAATTTTTTGTATTGCTGCTGAA	12	30	1
TTTTCAGATGATTTCTCGCTCTTTATGGCA	12	61	0
TGATATAGCCTTTTCTCGTCGAATTCTATT	14	114	0
          **********
MAP Score: 8.84778

Motif 4
TATAATATATAAAAGCCTTTTTCCGCTTTTA	9	171	0
AAATCATCTGAAAAGCATTTTAAATCCCTAA	12	77	1
ATCCCAAATAAAAAGCTTTATAAAAACAAAC	9	27	0
ACTTTTAAAAAAAGGCGTTTTTAGCGAGAAA	9	76	0
ATATGTTAATCAAAGCAATTTC         	2	38	1
GCACCAAAATCAAAGCTTTATTATTCTCAAC	7	38	1
TTCGACGAGAAAAGGCTATATCAGCCAGATA	14	121	1
     AACGGAAAAACGTTTTAAATCAGCTG	0	5	1
AAACCGGTAAAAAAGGTATTTAAGAGAGAAA	6	71	1
ATTTTAAAAATAAGACATTATCG        	12	2	0
          ****** ****
MAP Score: 7.40529

Motif 5
   AACGGAAAAACGTTTTAAATCAGCTGATTAA	0	7	1
TATATTTGATTAATCTTCTAAATCACATAAATTG	6	33	1
CCCAAATAAAAAGCTTTATAAAAACAAACAGTCG	9	22	0
CTGTGGAGTTTATACTTTTAAAAAAAGGCGTTTT	9	86	0
AAAGCGGAAAAAGGCTTTTATATATTATAAGCCA	9	173	1
TTTCTTTTCCAAAAAATTTAAATAGTAAC     	10	5	0
GAAATTCCGAAAATTTTTTATATTGAAAAATTGA	10	35	1
ATTTAAACGGAATCCTTATAAATCGAGAACCGAT	11	98	1
CAAAAAATTTAATTATTTTAAAAATAAGACATTA	12	13	0
ATCATCTGAAAAGCATTTTAAATCCCTAATTCCA	12	79	1
GTTTAGGTTTTAAGGTTCTAAATCGATCTGCCTT	13	13	0
          **   ** ******
MAP Score: 7.12312

Motif 6
AACCACCAACAAGAGAGGAAATCGACACACT	5	224	1
AAAGGTATTTAAGAGAGAAAAATCTGCCGTT	6	82	1
TCAAACTTATAAAAGCGGAAAAAGGCTTTTA	9	162	1
AACTGCCATAAAGAGCGAGAAATCATCTGAA	12	58	1
TCAATCAAAAAAGAAAGGAAAACTTTAAATA	8	214	1
TTTGCTCATCAAAACCGTAAACACCAATCTG	5	88	0
TATAAGTTTGAAAACCGGAAATCGCTTAAGA	9	142	0
TTTTAATAAGAAAAAAGTGAAGGAGGTGTAT	5	278	1
TGGAATTTCCAAAAAAGCAAGCATAAAAACT	8	162	1
CACAGCAGAGAAAAGAGAACGATCGTAACGC	14	13	1
TGAGCAAACGAAGAGAATGAAGCTCTTAGCG	5	111	1
          ******* ***
MAP Score: 7.0991

Motif 7
TTCTGGACTTCCGGAAGGCACTGGCCCCTACAGGGTG	5	45	1
TTGAAATTATCATCCCGGAGGAAGTCGAGTACACCGA	5	188	1
TCAGCCCCGGCTATGAGGCGTTAGGCCGGGGTTGCCG	8	12	1
GGTTGCCGAGCGGTAAGGCGCACGCCTGGAGAGCGTG	8	41	1
GATTCGAACCCACGCGGGCGAACGCCCACACGCTCTC	8	69	0
GATGTGCAGGCAGAATGGCGGAAGTCCTTTTGGTTTC	10	99	1
CTTCAACCGCCGCTAAGGCTGATGACGCCTGTTCTCA	11	23	0
CTAATTGAATCGGTATGGGTGATGGCGTCCACCTTCA	11	55	0
          *   * **** * * **
MAP Score: 6.48947

Motif 8
         ACAACTCCCGGATACCTCGAC	5	1	1
       ATTCAGCCCCGGCTATGAGGCGT	8	3	1
TACCGCTCGGCAACCCCGGCCTAACGCCTC	8	26	0
GGTGGGATTCGAACCCACGCGGGCGAACGC	8	81	0
GTTCGAATCCCACCCCCGGCGCTGTTGTAT	8	97	1
CGTCCACCTTCAACCGCCGCTAAGGCTGAT	11	37	0
GCAGAACCTTCTGCCCCCTCTACAACTTAA	14	86	1
          **********
MAP Score: 6.36237

Motif 9
      AACGGAAAAACGTTTTAAATCAGCTGAT	0	4	1
TTTTAATAAGAAAAAAGTGAAGGAGGTGTATT  	5	278	1
ATAAACCGGTAAAAAAGGTATTTAAGAGAGAAAA	6	69	1
AAAAAGAAAGGAAAACTTTAAATAGTAATTATTT	8	221	1
ATCCCAAATAAAAAGCTTTATAAAAACAAACAGT	9	24	0
TACTTTTAAAAAAAGGCGTTTTTAGCGAGAAATA	9	74	0
TAAAAGCGGAAAAAGGCTTTTATATATTATAAGC	9	171	1
TTTCTTTTCCAAAAAATTTAAATAGTAAC     	10	5	0
AAGAAATTCCGAAAATTTTTTATATTGAAAAATT	10	33	1
AATCGAACTTAAAAGGTGGTTGGATGTGCAGGCA	10	77	1
GCAGCAATACAAAAAATTTAATTATTTTAAAAAT	12	22	0
AAATCATCTGAAAAGCATTTTAAATCCCTAATTC	12	77	1
CGCTGCTTAGAAAAACCGTTACAAGACTCAAAGA	14	41	1
          *****  ****  *
MAP Score: 5.96627

Motif 10
         ACAACTCCCGGATACCTCGAC	5	1	1
AGAAAGTTCTGGACTTCCGGAAGGCACTGG	5	39	1
TCGGTGTACTCGACTTCCTCCGGGATGATA	5	195	0
TTAAGTGTGTCGATTTCCTCTCTTGTTGGT	5	228	0
TACCGCTCGGCAACCCCGGCCTAACGCCTC	8	26	0
GGTGGGATTCGAACCCACGCGGGCGAACGC	8	81	0
GGTTCGAATCCCACCCCCGGCGCTGTTGTA	8	96	1
TTTTCTTAAGCGATTTCCGGTTTTCAAACT	9	139	1
GAAACCAAAAGGACTTCCGCCATTCTGCCT	10	106	0
CGTCCACCTTCAACCGCCGCTAAGGCTGAT	11	37	0
          **********
MAP Score: 5.71768

Motif 11
ATTTAAACGGAATCCTTATAAATCGAGAACCGATATCG	11	98	1
TGCTTAGAAAAACCGTTACAAGACTCAAAGACAAATCA	14	44	1
ATCATCTGAAAAGCATTTTAAATCCCTAATTCCACCAG	12	79	1
TCCGGTTTTCAAACTTATAAAAGCGGAAAAAGGCTTTT	9	154	1
   AACGGAAAAACGTTTTAAATCAGCTGATTAACTCG	0	7	1
CCCAAATAAAAAGCTTTATAAAAACAAACAGTCGAACA	9	18	0
CCAAAAAAGCAAGCATAAAAACTCATGTTTTATTCGTA	8	170	1
ACCAAAATCAAAGCTTTATTATTCTCAACCAGATTGTT	7	40	1
ATATTTGATTAATCTTCTAAATCACATAAATTGACATA	6	34	1
GCCTTTTTTTAAAAGTATAAACTCCACAGTAGTTTTTT	9	91	1
AATAATCCCCAAACGACATAATCCCAAATAAAAAGCTT	9	40	0
          ** * *** **  *   *
MAP Score: 3.05869

Motif 12
CGGCGAGTTAATCAGCTGATTTAAAACGTTTTTCCGTT         	0	1	0
AAGAGCTTCATTCTCTTCGTTTGCTCATCAAAACCGTAAACACCAAT	5	91	0
CGTGTTGAATAACAGCTCTTTTGAAATTATCATCCCGGAGGAAGTCG	5	168	1
AAGAGAGGAAATCGACACACTTAAAGAATTGGACCCGGATGGTATTT	5	234	1
CGGCAGATTTTTCTCTCTTAAATACCTTTTTTACCGGTTTATGTCAA	6	64	0
      ATTCAGCCCCGGCTATGAGGCGTTAGGCCGGGGTTGCCGAG	8	4	1
AAAAGCCTTTTTCCGCTTTTATAAGTTTGAAAACCGGAAATCGCTTA	9	145	0
GGTGGACGCCATCACCCATACCGATTCAATTAGCCCGGTATTTAAAC	11	59	1
AGAGCGAGAAATCATCTGAAAAGCATTTTAAATCCCTAATTCCACCA	12	69	1
TCAAAGACAAATCAATAGGCAGAACCTTCTGCCCCCTCTACAACTTA	14	68	1
          ***  *       *     *   ****
MAP Score: 1.86904