AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_operons019_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243036
 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	AF1540	143	succinyl-CoA synthetase, beta subunit (sucC-1)
#10	AF1938	112	conserved hypothetical protein
#11	AF2186	65	succinyl-CoA synthetase, beta subunit (sucC-2)
#12	AF2187	174	A. fulgidus predicted coding region AF2187

Motif 1
  AACGGAAAAACGTTTTAAATCAGCTGATTAA	0	8	1
AATCAAATATAATAAGTTAAATCCTATCTGTGA	6	11	0
ATATTTGATTAATCTTCTAAATCACATAAATTG	6	34	1
AAAAGAAAGGAAAACTTTAAATAGTAATTATTT	8	222	1
TTCTTTTCCAAAAAATTTAAATAGTAAC     	9	5	0
TGAAAAATTGAGAATGTTAAATCGAACTTAAAA	9	58	1
CAGCAATACAAAAAATTTAATTATTTTAAAAAT	10	22	0
TCATCTGAAAAGCATTTTAAATCCCTAATTCCA	10	80	1
TTTAGGTTTTAAGGTTCTAAATCGATCTGCCTT	11	13	0
ATTCGACGAGAAAAGGCTATATCAGCCAGATAT	12	120	1
          **   ********
MAP Score: 9.25

Motif 2
TTTAATTTTTATTTTTTCCAACAGATAGTTA	4	11	1
TGAATAACAGCTCTTTTGAAATTATCATCCC	5	173	1
ACCTCCTTCACTTTTTTCTTATTAAAATACC	5	274	0
          CTTTTTTCGAATTATTTTCTA	7	0	1
TTTATGCTTGCTTTTTTGGAAATTCCACAGA	8	158	0
GTTTTCCTTTCTTTTTTGATTGATTATTATA	8	206	0
TACTATTTAAATTTTTTGGAAAAGAAATTCC	9	12	1
AATTCCGAAAATTTTTTATATTGAAAAATTG	9	37	1
AAATAATTAAATTTTTTGTATTGCTGCTGAA	10	29	1
          ******** **
MAP Score: 7.03767

Motif 3
          AACGGAAAAACGTTTTAAATC	0	0	1
     AGCCAACAGGGAGATTTCTCATTACT	4	49	0
     TGGAGAACGGCAGATTTTTCTCTCTT	6	92	0
GTTGAATCTTACCGGAAAATTACTTCTGTGG	8	134	1
ATCAAAAAAGAAAGGAAAACTTTAAATAGTA	8	217	1
GTAATTATTTATCGGGAAATTC         	8	245	1
TGCCATAAAGAGCGAGAAATCATCTGAAAAG	10	61	1
        AGAAAGGCAGATCGATTTAGAAC	11	2	1
TACAAGACTCAAAGACAAATCAATAGGCAGA	12	60	1
AGACAAATCAATAGGCAGAACCTTCTGCCCC	12	72	1
          * *********
MAP Score: 5.96619

Motif 4
GTTCTGGACTTCCGGAAGGCACTGGCCCCTACAGGGTG	5	44	1
TTTGAAATTATCATCCCGGAGGAAGTCGAGTACACCGA	5	187	1
TTCAGCCCCGGCTATGAGGCGTTAGGCCGGGGTTGCCG	8	11	1
GGGTTGCCGAGCGGTAAGGCGCACGCCTGGAGAGCGTG	8	40	1
CGCCTGGAGAGCGTGTGGGCGTTCGCCCGCGTGGGTTC	8	63	1
GGATGTGCAGGCAGAATGGCGGAAGTCCTTTTGGTTTC	9	98	1
          **     **** * * **
MAP Score: 5.44594

Motif 5
          CAACCAGAAATGAAGGGTGAA	1	11	0
TTTATTTTTTCCAACAGATAGTTAAAGTATA	4	18	1
    AGCCAACAGGGAGATTTCTCATTACTT	4	48	0
ACAGGGTGATAACGCAGATTGGTGTTTACGG	5	74	1
    TGGAGAACGGCAGATTTTTCTCTCTTA	6	91	0
TTATTATTCTCAACCAGATTGTTTCT     	7	55	1
GTTGGATGTGCAGGCAGAATGGCGGAAGTCC	9	95	1
       AGAAAGGCAGATCGATTTAGAACC	11	3	1
AAGGCTATATCAGCCAGATATAGCAGCAATA	12	132	1
          ********* *
MAP Score: 4.30596

Motif 6
AATGAGAAATCTCCCTGTTGGCT        	4	52	1
AAGTTCTGGACTTCCGGAAGGCACTGGCCCC	5	42	1
TCTGCGTTATCACCCTGTAGGGGCCAGTGCC	5	61	0
TACTCGACTTCCTCCGGGATGATAATTTCAA	5	188	0
TAAAGAATTGGACCCGGATGGTATTTTAATA	5	255	1
    ATTCAGCCCCGGCTATGAGGCGTTAGG	8	6	1
TGAGGCGTTAGGCCGGGGTTGCCGAGCGGTA	8	25	1
TGTGGGCGTTCGCCCGCGTGGGTTCGAATCC	8	76	1
ATACAACAGCGCCGGGGGTGGGATTCGAACC	8	96	0
          * *********
MAP Score: 4.2789

Motif 7
AAAATTACAGCAAAATAGTAATATATATGTT	2	14	1
ACCTCGACGGTAGCAGAGAAAGTTCTGGACT	5	23	1
GAACCACCAACAAGAGAGGAAATCGACACAC	5	223	1
CATAAACCGGTAAAAAAGGTATTTAAGAGAG	6	68	1
AAAAGGTATTTAAGAGAGAAAAATCTGCCGT	6	81	1
GTGGAATTTCCAAAAAAGCAAGCATAAAAAC	8	161	1
AATAATCAATCAAAAAAGAAAGGAAAACTTT	8	209	1
AAGGAAAACTTTAAATAGTAATTATTTATCG	8	228	1
TCCAAAAAATTTAAATAGTAAC         	9	1	0
     AAACACAGCAGAGAAAAGAGAACGAT	12	5	1
          ******** **
MAP Score: 4.21573

Motif 8
GAGAAATCTCCCTGTTGGCT          	4	55	1
ACGTTGAGGACGTGTTGAATAACAGCTCTT	5	158	1
CCTCATAGCCGGGGCTGAAT          	8	0	0
AACAGCGCCGGGGGTGGGATTCGAACCCAC	8	93	0
CACCCCCGGCGCTGTTGTATCTTGGCTGTT	8	107	1
TTGTATCTTGGCTGTTGAATCTTACCGGAA	8	121	1
GAAAATTACTTCTGTGGAATTTCCAAAAAA	8	148	1
AACTTAAAAGGTGGTTGGATGTGCAGGCAG	9	82	1
TTTTTGTATTGCTGCTGAACTGCCATAAAG	10	41	1
     GAAGGCTGGTGGAATTAGGGATTTA	10	97	0
          **********
MAP Score: 2.59069

Motif 9
CGGATACCTCGACGGTAGCAGAGAAAGTTCTGGACTTCCGG	5	18	1
TTGGCTGTTGAATCTTACCGGAAAATTACTTCTGTGGAATT	8	128	1
AATTTCCAAAAAAGCAAGCATAAAAACTCATGTTTTATTCG	8	165	1
TAATCAATCAAAAAAGAAAGGAAAACTTTAAATAGTAATTA	8	211	1
TTTTTTGGAAAAGAAATTCCGAAAATTTTTTATATTGAAAA	9	23	1
TGAGAATGTTAAATCGAACTTAAAAGGTGGTTGGATGTGCA	9	66	1
TAAAGAGCGAGAAATCATCTGAAAAGCATTTTAAATCCCTA	10	66	1
          AAACACAGCAGAGAAAAGAGAACGATCGTAA	12	0	1
AACTTAATAGAATTCGACGAGAAAAGGCTATATCAGCCAGA	12	109	1
          **    * * *****     *
MAP Score: 0.663611

Motif 10
ATACTTTAACTATCTGTTGGAAAAAATAAAAATTAAAA     	4	5	0
TGGACCCGGATGGTATTTTAATAAGAAAAAAGTGAAGGAGGTG	5	263	1
TTATATTTGATTAATCTTCTAAATCACATAAATTGACATAAAC	6	32	1
ATTTTCGGAATTTCTTTTCCAAAAAATTTAAATAGTAAC    	9	6	0
  CGATAATGTCTTATTTTTAAAATAATTAAATTTTTTGTATT	10	8	1
TTTAACATTCTCAATTTTTCAATATAAAAAATTTTCGGAATTT	9	36	0
CTTGCTTTTTTGGAAATTCCACAGAAGTAATTTTCCGGTAAGA	8	140	0
AAAAGAAAGGAAAACTTTAAATAGTAATTATTTATCGGGAAAT	8	222	1
          *     **  * *  * * ** *
MAP Score: 0.476956