AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_fusions011_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241340
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF0074	261	biotin operon repressor/biotin--[acetyl CoA carboxylase] ligase (birA)
#1	AF0075	26	conserved hypothetical protein
#2	AF0154	139	conserved hypothetical protein
#3	AF0155	62	A. fulgidus predicted coding region AF0155
#4	AF0688	228	iron-sulfur cluster binding protein
#5	AF1186	139	conserved hypothetical protein
#6	AF1461	87	iron-sulfur cluster binding protein, putative
#7	AF1643	50	conserved hypothetical protein
#8	AF1644	35	tungsten formylmethanofuran dehydrogenase, subunit F (fwdF)

Motif 1
TTTGTAATACAAAATTAAAAATCGAAGAGAG	0	39	0
TGTATTACAAAAAAGTAAATACTCATAAAGC	0	59	1
GCTTGAGGAAAAAAGGGTTTATTAAGATTAT	0	225	1
          AAAATTTTTAGTATATCCTTT	1	0	1
      TGGTAAAAGGATATACTAAAAATTT	1	11	0
ACTGTTAGGTAACAGTGTTTGGGGTGGTGAT	2	13	0
ACTGTTACCTAACAGTGTTTATATTTAACAT	2	28	1
GTTTATATTTAACATTATAAGCATTATGCAT	2	44	1
AATGCAATCAAAAATGCATAATGCTTATAAT	2	57	0
CCTAAATTTAAAAAGTTTTTGGTTGGCCTAA	2	101	0
AAATTTTTTTAAAATTAAAAATTGACACCAA	4	13	0
AACTATATCGCAAATGCTATAGATTTGTATA	4	171	0
CTTTTCTCCGCAAATTATATAACTATATCGC	4	191	0
ATTTGCGGAGAAAAGGCTATGAGGTGAAAGC	4	207	1
TGTTGGTAATCAAATTCTTAAGGATTGAGAT	5	58	0
CAAACATTACAAAAGTTTATATACCTCAGCC	5	105	1
AAGGGTGTTTAAAAGGTTTTAGAGTTGAGCG	7	24	1
 CAAAGGGTTAAAAGGCTAAGAATAAAGGTG	8	9	1
          ****** ****
MAP Score: 17.3396

Motif 2
CGATTAAGGCAGCTTACTCGTT         	0	1	0
ATACTCATAAAGCTCATACCTAAGCAATCCC	0	77	1
TACCTAAGCAATCCCAATCTTGGAAAAGCCC	0	93	1
ATCTTGGAAAAGCCCAATTAACCCACCTTAA	0	109	1
AACCCCCGCGGGCCCATTTTTAAGGTGGGTT	0	128	0
TGTTTAGGATAGCCTAAATTTAAAAAGTTTT	2	113	0
AATTTAGGCTATCCTAAACATAACG      	2	124	1
TCAATTTTCCTGCCCATTTCTTCCAGCCTTC	4	103	1
CACACTTCTTTGCTCAATCTTATCTCAATCC	5	37	1
GCTCAATCTTATCTCAATCCTTAAGAATTTG	5	48	1
AATTTAAAGCAGCTCAAACATTACAAAAGTT	5	91	1
TATATACCTCAGCCCACTTCACATTAC    	5	122	1
         GAGCCCAATTAGACGGGGAAGT	6	1	1
          ********* *
MAP Score: 8.95785

Motif 3
CTCTCTTCGATTTTTAATTTTGTATTACAAA	0	39	1
AACCAAAAACTTTTTAAATTTAGGCTATCCT	2	108	1
ATAGTAAATTTTTTTAAAATTAAAAATTGAC	4	18	0
CGCGGGCCCATTTTTAAGGTGGGTTAATTGG	0	122	0
TATATAAACTTTTGTAATGTTTGAGCTGCTT	5	97	0
        TTTTTTTCATATTCGAAGATTTT	3	2	1
AAAAAAGGGTTTATTAAGATTATGGTGTTGT	0	233	1
ACAGTGTTTATATTTAACATTATAAGCATTA	2	39	1
CTAAAATCGGTTTTGAAAATGCAATCAAAAA	2	74	0
          ******* ***
MAP Score: 5.29012

Motif 4
    AACGAGTAAGCTGCCTTAATCGATTTCTCCTCT	0	6	1
AGCTCATACCTAAGCAATCCCAATCTTGGAAAAGCCC	0	87	1
AAAGCCCAATTAACCCACCTTAAAAATGGGCCCGCGG	0	117	1
GGGCCCTCAGTCAGCTTGAGGAAAAAAGGGTTTATTA	0	212	1
      CCCATCACCACCCCAAACACTGTTACCTAAC	2	4	1
AAACCGATTTTAGGCCAACCAAAAACTTTTTAAATTT	2	92	1
TTTTTAAATTTAGGCTATCCTAAACATAACG      	2	118	1
TCCAACTTAGTCAGCAATCAACATCTACCTTTTCCCT	3	33	0
TTTATATACCTCAGCCCACTTCACATTAC        	5	120	1
          *****   *  ** * *
MAP Score: 5.25447

Motif 5
AGCTGCCTTAATCGATTTCTCCTCTCTTCG	0	18	1
TTCTCCTCTCTTCGATTTTTAATTTTGTAT	0	34	1
ACCCCCGCGGGCCCATTTTTAAGGTGGGTT	0	128	0
ATCTTAATAAACCCTTTTTTCCTCAAGCTG	0	223	0
TATAAGCATTATGCATTTTTGATTGCATTT	2	59	1
GCATTTTTGATTGCATTTTCAAAACCGATT	2	71	1
  GTATTGGTGTCAATTTTTAATTTTAAAA	4	8	1
AATCAATATAGTAAATTTTTTTAAAATTAA	4	26	0
CTTGCAAAACATCAATTTTCCTGCCCATTT	4	92	1
CAATTTTCCTGCCCATTTCTTCCAGCCTTC	4	104	1
TGCATCAAAAGTCCATTCTCTTTATAAACT	6	29	0
GACTTTTGATGCACATTTTCCTTTCTTCCC	6	46	1
          **********
MAP Score: 4.35815

Motif 6
GTATTACAAAAAAGTAAATACTCATAAAGCTC	0	60	1
GAGAGATACAACACCATAATCTTAATAAACCC	0	239	0
   AAAATTTTTAGTATATCCTTTTACCA   	1	7	1
 CCCATCACCACCCCAAACACTGTTACCTAAC	2	9	1
GATTTTAGGCCAACCAAAAACTTTTTAAATTT	2	97	1
ATCTACCTTTTCCCTAAAATCTTCGAATATGA	3	16	0
AGACTGTAGCTCATCATATACTATACAAATCT	4	150	1
ATATAACTATATCGCAAATGCTATAGATTTGT	4	174	0
TAGCCTTTTCTCCGCAAATTATATAACTATAT	4	194	0
    GCTTTCACCTCATAGCCTTTTCTCCGCA	4	210	0
TTACTGTTGGTAATCAAATTCTTAAGGATTGA	5	61	0
AAGTCCATTCTCTTTATAAACTTCCCCGTCTA	6	19	0
AATTCGCTCAACTCTAAAACCTTTTAAACACC	7	27	0
          ********  **
MAP Score: 1.02295

Motif 7
TACTCATAAAGCTCATACCTAAGCAATCCC	0	78	1
TCAGGCGAGCGCTCTAACCAGGCTGAGCCA	0	181	1
CCTTCCAGCAGCTCCTCCATCAGACTGTAG	4	129	1
ACACTTCTTTGCTCAATCTTATCTCAATCC	5	38	1
CTCAATCTTATCTCAATCCTTAAGAATTTG	5	49	1
ATTTAAAGCAGCTCAAACATTACAAAAGTT	5	92	1
          **********
MAP Score: 0.110106

Motif 8
AAATACTCATAAAGCTCATACCTAAGCAATC	0	75	1
CTGAGCCACGGGCCCTCAGTCAGCTTGAGGA	0	203	1
CAGCCTTCCAGCAGCTCCTCCATCAGACTGT	4	126	1
CCATCAGACTGTAGCTCATCATATACTATAC	4	145	1
GTAATTTAAAGCAGCTCAAACATTACAAAAG	5	89	1
AAAAGTTTATATACCTCAGCCCACTTCACAT	5	115	1
CGCTTTTATAGCACCTCAGCGA         	6	75	1
          * *********
MAP Score: 0.105604