AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_fusions004_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241122
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF0006	104	corrinoid methyltransferase protein (mtaC-1)
#1	AF0008	73	oxalate/formate antiporter (oxlT-1)
#2	AF0014	95	A. fulgidus predicted coding region AF0014
#3	AF0016	54	A. fulgidus predicted coding region AF0016
#4	AF0018	22	3-ketoacyl-CoA thiolase (acaB-1)
#5	AF0021	38	signal-transducing histidine kinase
#6	AF0409	74	aspartate aminotransferase (aspB-4)
#7	AF0410	56	signal-transducing histidine kinase, putative
#8	AF1045	86	methyl-accepting chemotaxis protein (tlpC-2)
#9	AF1049	102	type II secretion system protein (gspE-4)
#10	AF1384	189	response regulator
#11	AF1515	199	signal-transducing histidine kinase
#12	AF1638	31	ribulose bisphosphate carboxylase, large subunit (rbcL-2)
#13	AF1639	30	signal-transducing histidine kinase
#14	AF2420	40	signal-transducing histidine kinase, putative
#15	AF2421	58	leucyl-tRNA synthetase (leuS)
#16	AF2425	85	methanol dehydrogenase regulatory protein (moxR)

Motif 1
ATAACAAAATTATCTGACTTTTGATTAAAAT	0	22	0
AACTGATTCATAACAGCTTTTATCTTTAGAA	0	54	1
GAAGGCCTATTTTCTAATTTGGAGGTGTTTA	0	82	1
AACCAGTTCATAACAGCCTTTATTTAGCACT	1	26	1
CAAATCATTTTATAAAATTTTTTTTAATTAA	2	16	1
AAATTTTTTTTAATTAACTTTTTGTTGTTAA	2	30	1
         TTTTTAACTTTTCTTTGTCAAT	3	1	1
GTGCAAAATTTAAGAAGTTTTCC        	5	2	0
CTTTCGAATATATCAACTTTTACCCGAATAA	6	39	0
GGACGATGAATATAAACTTTGCTGTTCAGTT	7	19	0
AATTTTCTTATTCGAAATTTTACTTTATAGA	8	21	1
CTGATGTTGCTATTAACCTTTGCTTTCATTT	9	41	0
ACCTCTTTAATTTCAGCTTTGGGAATCAGCG	10	54	0
TCCTCAACATTTAAAAATTTTACTATCTCTT	10	155	0
         TTACCTAATTTTATCCTCAACA	10	177	0
TTATAATATATAAAAGCCTTTTTCCGCTTTT	11	16	1
TTTTCCGCTTTTATAAGTTTGAAAACCGGAA	11	35	1
GTTTTTTGCTTAAGTAGTTTTCTTAAGCGAT	11	66	0
TACTGTGGAGTTTATACTTTTAAAAAAAGGC	11	97	1
TAATCCCAAATAAAAAGCTTTATAAAAACAA	11	159	1
      AATTTTTTAAATTTTTTGAGTACTT	13	4	1
AATTCAAAAATAAAAAACTTTTTGA      	14	4	0
TAAATGGGATTAAAAAATTTGGCGTTTGGCC	15	24	0
          *** *******
MAP Score: 22.2875

Motif 2
GAACTGATTCATAACAGCTTTTATCTTTAGAAGG	0	53	1
GAACCAGTTCATAACAGCCTTTATTTAGCACTCA	1	25	1
ATAATCCCAAATAAAAAGCTTTATAAAAACAAAC	11	158	1
AAAGTTAATTAAAAAAAATTTTATAAAATGATTT	2	17	0
CTTATAATATATAAAAGCCTTTTTCCGCTTTTAT	11	15	1
TTTACTTTATAGAGAAAATTTTATTTTTTATTTT	8	39	1
ATTTAACTGAACAGCAAAGTTTATATTCATCGTC	7	15	1
AAATTCAAAAATAAAAAACTTTTTGA        	14	2	0
TTCTAAAGAGATAGTAAAATTTTTAAATGTTGAG	10	150	1
TATACTTTTAAAAAAAGGCGTTTTTAGCGAGAAA	11	109	1
TATAAACTCCACAGTAGTTTTTTGCTTAAGTAGT	11	79	0
          * ** **  *****
MAP Score: 15.0605

Motif 3
TGTTTTTATAAAGCTTTTTATTTGGGATTATG	11	157	0
TTTGCACCACAATCTTTTGTTT          	5	26	1
     TCAAAAAGTTTTTTATTTTTGAATTTC	14	5	1
TACACTTCTGAATTTTCTTATTCGAAATTTTA	8	11	1
AGAGATAGTAAAATTTTTAAATGTTGAGGATA	10	156	1
          AATTTTTTAAATTTTTTGAGTA	13	0	1
GCCAAACGCCAAATTTTTTAATCCCATTTATT	15	25	1
      TTTTTAACTTTTCTTTGTCAATTATC	3	4	1
TAAAAAATAAAATTTTCTCTATAAAGTAAAAT	8	37	0
TTAGAAGGCCTATTTTCTAATTTGGAGGTGTT	0	79	1
GAGAAAATTTTATTTTTTATTTTCGCAATCTA	8	50	1
CAAGAACCTCAAGCTTCTGATATTTACGTTAT	6	11	1
TCATTTTATAAAATTTTTTTTAATTAACTTTT	2	20	1
TTCTTATTCGAAATTTTACTTTATAGAGAAAA	8	25	1
       GGAAAACTTCTTAAATTTTGCACCA	5	3	1
CTATTTCAGCAATCTGCTATTTGACGTTTCCC	16	14	1
AAGCGGAAAAAGGCTTTTATATATTATAAGCC	11	13	0
CAAAATTATCTGACTTTTGATTAAAATAACTT	0	17	0
  AATACCAGTAAGTTCTCTTTTTAATAACGA	3	34	0
ACTGAACAGCAAAGTTTATATTCATCGTCCAG	7	20	1
TGTTGCTATTAACCTTTGCTTTCATTTTTGGG	9	36	0
          ** ***** ***
MAP Score: 12.8496

Motif 4
       CGCGAATCCCCTCTTAAGCAGAG	1	60	0
AGGTGCAGTGTAATCCCAAAAATGAAAGCA	9	22	1
CAGCGATGTAGTATCCCTAAATTATTTCAC	10	29	0
CTACATCGCTGATTCCCAAAGCTGAAATTA	10	48	1
TAGCGAGAAATAATCCCCAAACGACATAAT	11	133	1
CCAAACGACATAATCCCAAATAAAAAGCTT	11	149	1
CCAAATTTTTTAATCCCATTTATTAGCCAC	15	33	1
GCTATTTGACGTTTCCCATAGCTCTAACCC	16	29	1
          **********
MAP Score: 5.87832

Motif 5
AGAAGGCCTATTTTCTAATTTGGAGGTGTTTA	0	81	1
ACAAATCATTTTATAAAATTTTTTTTAATTAA	2	15	1
TAACTTTTTGTTGTTAATTAATTATTTATCAG	2	44	1
          TTTTTAACTTTTCTTTGTCAAT	3	0	1
TAACTTTTCTTTGTCAATTATCGTTATTAAAA	3	14	1
   GGAAAACTTCTTAAATTTTGCACCACAAT	5	7	1
    TTACACTTCTGAATTTTCTTATTCGAAA	8	6	1
GAAAATTTTATTTTTTATTTTCGCAATCTACT	8	52	1
ATCCTCAACATTTAAAAATTTTACTATCTCTT	10	155	0
CTTTTTCCGCTTTTATAAGTTTGAAAACCGGA	11	33	1
       AATTTTTTAAATTTTTTGAGTACTT	13	3	1
  TCAAAAAGTTTTTTATTTTTGAATTTCCCT	14	8	1
          ** * *******
MAP Score: 5.4349

Motif 6
TCTCTGCTTAAGAGGGGATTCGCG         	1	59	1
ACTGAACAGCAAAGTTTATATTCATCGTCCAGA	7	20	1
TTTTCTCTATAAAGTAAAATTTCGAATAAGAAA	8	24	0
AAATGAAAGCAAAGGTTAATAGCAACATCAGTT	9	41	1
TCCACTACGTAGAGGTTGAACTCCTCTGGATTC	10	115	0
AACTTATAAAAGCGGAAAAAGGCTTTTATATAT	11	21	0
TAAGTTTGAAAACCGGAAATCGCTTAAGAAAAC	11	48	1
CCTTTTTTTAAAAGTATAAACTCCACAGTAGTT	11	94	0
AATAATCCCCAAACGACATAATCCCAAATAAAA	11	141	1
AGCTATGGGAAACGTCAAATAGCAGATTGCTGA	16	19	0
          *****  *** **
MAP Score: 0.856655