AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_fusions011_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241352
 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	AF1189	283	A. fulgidus predicted coding region AF1189
#7	AF1191	32	dihydroxynaphthoic acid synthase (menB)
#8	AF1192	50	conserved hypothetical protein
#9	AF1195	27	activator 1, replication factor C, 53 KD subunit
#10	AF1196	65	N5,N10-methylenetetrahydromethanopterin reductase (mer-2)
#11	AF1197	300	3-ketoacyl-CoA thiolase (fadA-2)
#12	AF1461	87	iron-sulfur cluster binding protein, putative
#13	AF1643	50	conserved hypothetical protein
#14	AF1644	35	tungsten formylmethanofuran dehydrogenase, subunit F (fwdF)

Motif 1
GCTTTATGAGTATTTACTTTTTTGTAATACA	0	59	0
ATAATCTTAATAAACCCTTTTTTCCTCAAGC	0	225	0
AAATTTTTAGTATATCCTTTTACCA      	1	11	1
ATCACCACCCCAAACACTGTTACCTAACAGT	2	13	1
ATGTTAAATATAAACACTGTTAGGTAACAGT	2	28	0
TTAGGCCAACCAAAAACTTTTTAAATTTAGG	2	101	1
GCTTTCACCTCATAGCCTTTTCTCCGCAAAT	4	207	0
GGCTGAGGTATATAAACTTTTGTAATGTTTG	5	105	0
TCTAAAATTTTCAATACTTTTTTCATACGAC	6	13	1
TTTAAAGCTTTTAACACTTTTCAATAGATTG	6	109	0
 AATACACCTCCTTCACTTTTTTCTTATTAA	11	280	0
CGCTCAACTCTAAAACCTTTTAAACACCCTT	13	24	0
CACCTTTATTCTTAGCCTTTTAACCCTTTG 	14	9	0
          **** ******
MAP Score: 13.8069

Motif 2
CCTCTCTTCGATTTTTAATTTTGTATTACAA	0	38	1
       AAAATTTTTAGTATATCCTTTTAC	1	3	1
         TTTTTTTCATATTCGAAGATTT	3	1	1
ATTGGTGTCAATTTTTAATTTTAAAAAAATT	4	12	1
TGGCAATATTATTTTTATTATATCACACTTC	5	14	1
 TCATCTAAAATTTTCAATACTTTTTTCATA	6	9	1
TTTTCAATACTTTTTTCATACGACTAATAAA	6	20	1
GTAGTCTTAAATTTTTCGTTCCATATTGCAT	6	234	0
     TTTTAATTTTTATTTTTTCCAACAGA	10	5	1
CCTCCTTCACTTTTTTCTTATTAAAATACCA	11	273	0
TTTGATGCACATTTTCCTTTCTTCCCGCTTT	12	50	1
          ******* ***
MAP Score: 10.026

Motif 3
TTAATAAACCCTTTTTTCCTCAAGCTGACT	0	220	0
ACCTCCTTCACTTTTTTCTTATTAAAATAC	11	275	0
TGCTGAATATCTTTTTTCTCAGAATATTTT	6	51	0
ATTTTCAATACTTTTTTCATACGACTAATA	6	19	1
TTTTCCAGTACATTTTTCCCTGCCCGGAG 	7	13	1
GCACATTTTCCTTTCTTCCCGCTTTTATAG	12	56	1
ATATATATTACTATTTTGCTGTAATTTTTA	8	12	0
TTATATCACACTTCTTTGCTCAATCTTATC	5	31	1
TGCAAAACATCAATTTTCCTGCCCATTTCT	4	94	1
  TGGCACACCTTTATTCTTAGCCTTTTAA	14	17	0
AAGCATTATGCATTTTTGATTGCATTTTCA	2	62	1
TGAGTATTTACTTTTTTGTAATACAAAATT	0	54	0
GCGCTAAGAGCTTCATTCTCTTCGTTTGCT	11	113	0
          **********
MAP Score: 8.64698

Motif 4
GATGGAGGAGCTGCTGGAAGGCTGGAAGAAA	4	119	0
          CTCCGGGCAGGGAAAAATGTA	7	21	0
AATGAGAAATCTCCCTGTTGGCT        	10	52	1
AAGTTCTGGACTTCCGGAAGGCACTGGCCCC	11	42	1
TCTGCGTTATCACCCTGTAGGGGCCAGTGCC	11	61	0
GCTCTTAGCGCTTCATGAAGGACGTAACGTT	11	132	1
ACTCGACTTCCTCCGGGATGATAATTTCAAA	11	187	0
TAAAGAATTGGACCCGGATGGTATTTTAATA	11	255	1
   GCTCAAGCTTCGGCAAGGGTGTTTAAAA	13	7	1
          **** ******
MAP Score: 7.23105

Motif 5
AGGTCCGGGGTTCGAACCCCCGCGGGCCCATTT	0	140	0
GGTTCGAACCCCGGACCTCTCGCTTATCAGGCG	0	155	1
CTCAGCCTGGTTAGAGCGCTCGCCTGATAAGCG	0	175	0
GGAGGAGCTGCTGGAAGGCTGGAAGAAATGGGC	4	114	0
CTGCTAACCCCTCGATAGCTGGAACTCATCATA	6	168	1
 TATACTCCTTTGGACGACTGGATTTGA     	9	9	1
   ACAACTCCCGGATACCTCGACGGTAGCAGA	11	7	1
AGAGAAAGTTCTGGACTTCCGGAAGGCACTGGC	11	37	1
TGTTGGTGGTTCGGTGTACTCGACTTCCTCCGG	11	202	0
          *****   *****
MAP Score: 6.58999

Motif 6
CTGCCTTAATCGATTTCTCCTCTCTTCGATTT	0	20	1
CTTAATAAACCCTTTTTTCCTCAAGCTGACTG	0	219	0
TCAACATCTACCTTTTCCCTAAAATCTTCGAA	3	21	0
TGCAAAACATCAATTTTCCTGCCCATTTCTTC	4	94	1
ATTTTCCTGCCCATTTCTTCCAGCCTTCCAGC	4	106	1
CACCTCATAGCCTTTTCTCCGCAAATTATATA	4	201	0
ATTTTCAATACTTTTTTCATACGACTAATAAA	6	19	1
TGCTGAATATCTTTTTTCTCAGAATATTTTTT	6	49	0
TTTTCCAGTACATTTTTCCCTGCCCGGAG   	7	13	1
TCGGTGTACTCGACTTCCTCCGGGATGATAAT	11	193	0
TTAAGTGTGTCGATTTCCTCTCTTGTTGGTGG	11	226	0
TTTTGATGCACATTTTCCTTTCTTCCCGCTTT	12	49	1
          * ******** *
MAP Score: 6.38726

Motif 7
ATACTCATAAAGCTCATACCTAAGCAATCC	0	77	1
TACCTAAGCAATCCCAATCTTGGAAAAGCC	0	93	1
ATCTTGGAAAAGCCCAATTAACCCACCTTA	0	109	1
 CCCATCACCACCCCAAACACTGTTACCTA	2	9	1
TCAATTTTCCTGCCCATTTCTTCCAGCCTT	4	103	1
CACACTTCTTTGCTCAATCTTATCTCAATC	5	37	1
GCTCAATCTTATCTCAATCCTTAAGAATTT	5	48	1
AATTTAAAGCAGCTCAAACATTACAAAAGT	5	91	1
TATATACCTCAGCCCACTTCACATTAC   	5	122	1
CTTTAAAATATCCCCAATCAGGAATTGGGG	6	133	1
TAGCAGTCTTTCCCCAATTCCTGATTGGGG	6	144	0
         GAGCCCAATTAGACGGGGAAG	12	1	1
          **********
MAP Score: 5.99784

Motif 8
 AACGAGTAAGCTGCCTTAATCGATTTCTCCTCT	0	9	1
ATGAGTATTTACTTTTTTGTAATACAAAATTAAA	0	51	0
AAGCTGTCATGCTGTCTTGCAAAACATCAATTTT	4	77	1
ATTATATCACACTTCTTTGCTCAATCTTATCTCA	5	30	1
TAATGTTTGAGCTGCTTTAAATTACTGTTGGTAA	5	80	0
AAAATTTAAGACTACTTTAATTTAGTATAGCAAG	6	250	1
CATATATATTACTATTTTGCTGTAATTTTTAAT 	8	9	0
       GAAATTGCTTTGATTAACATATATATT	8	33	0
       TATACTCCTTTGGACGACTGGATTTGA	9	3	1
TTGAATAACAGCTCTTTTGAAATTATCATCCCGG	11	172	1
          *** ***** *  *
MAP Score: 2.88312

Motif 9
AGTAAATACTCATAAAGCTCATACCTAAGC	0	72	1
TTCCAGCCTTCCAGCAGCTCCTCCATCAGA	4	123	1
CCTCCATCAGACTGTAGCTCATCATATACT	4	142	1
ACAGTAATTTAAAGCAGCTCAAACATTACA	5	86	1
AAACGAAGAGAATGAAGCTCTTAGCGCTTC	11	116	1
TTACGTCCTTCATGAAGCGCTAAGAGCTTC	11	129	0
GACGTGTTGAATAACAGCTCTTTTGAAATT	11	166	1
          AATACACCTCCTTCACTTTT	11	290	0
TCCCGCTTTTATAGCACCTCAGCGA     	12	72	1
          **********
MAP Score: 2.87425

Motif 10
GCCTTAATCGATTTCTCCTCTCTTCGATTTTT	0	22	1
TGCAAAACATCAATTTTCCTGCCCATTTCTTC	4	94	1
TTTCCTGCCCATTTCTTCCAGCCTTCCAGCAG	4	108	1
ATTTTCAATACTTTTTTCATACGACTAATAAA	6	19	1
ATATTGCATTCTTTCATCCACCCCCCAATAAC	6	211	0
TTTCCAGTACATTTTTCCCTGCCCGGAG    	7	14	1
TTTAATTTTTATTTTTTCCAACAGATAGTTAA	10	11	1
GCACATTTTCCTTTCTTCCCGCTTTTATAGCA	12	56	1
          *********  *
MAP Score: 2.44484

Motif 11
AAAAATCCCGCTTGGACAATCTATTGAAAAGTGTTAAAAG	6	93	1
TTTTGGTTGGCCTAAAATCGGTTTTGAAAATGCAATCAAA	2	76	0
AAGAATTGGACCCGGATGGTATTTTAATAAGAAAAAAGTG	11	257	1
AAGGACGTAACGTTGAGGACGTGTTGAATAACAGCTCTTT	11	149	1
TTATTAGTCGTATGAAAAAAGTATTGAAAATTTTAGATGA	6	10	0
TCGACTTCCTCCGGGATGATAATTTCAAAAGAGCTGTTAT	11	176	0
ATTACTTATACTTTAACTATCTGTTGGAAAAAATAAAAAT	10	15	0
TATCTTTTTTCTCAGAATATTTTTTTATTAGTCGTATGAA	6	34	0
  GAGAGATACAACACCATAATCTTAATAAACCCTTTTTT	0	233	0
  GCTCAAGCTTCGGCAAGGGTGTTTAAAAGGTTTTAGAG	13	8	1
GTTTGAGCTGCTTTAAATTACTGTTGGTAATCAAATTCTT	5	70	0
ATTTACTTTTTTGTAATACAAAATTAAAAATCGAAGAGAG	0	39	0
TACGAATCAATATAGTAAATTTTTTTAAAATTAAAAATTG	4	20	0
      TTCTTGGCAATATTATTTTTATTATATCACACTT	5	4	1
  GAGCCCAATTAGACGGGGAAGTTTATAAAGAGAATGGA	12	8	1
          *   **     * ** ****
MAP Score: 2.15462