AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_fusions018_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241561
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF0106	116	aspartate carbamoyltransferase, catalytic subunit (pyrB)
#1	AF1255	27	ornithine carbamoyltransferase (argF)
#2	AF1259	36	inosine monophosphate dehydrogenase, putative
#3	AF1260	207	phosphoribosylformylglycinamidine synthase I (purQ)
#4	AF1261	133	medium-chain acyl-CoA ligase (alkK-4)
#5	AF1263	74	iron-sulfur cluster binding protein
#6	AF1269	300	A. fulgidus predicted coding region AF1269
#7	AF1270	33	transcriptional regulatory protein, ArsR family
#8	AF2251	30	competence-damage protein, putative
#9	AF2252	78	argininosuccinate synthetase (argG)

Motif 1
CATACGGGAGAAAGTTTAAAACCGTAAAAGG	0	86	1
AGATTAAACAAAAGTTAAAAAACTTCCTGGG	9	22	0
CGACACGGAAAAAGCTTAAAAGATTGCGGTT	3	174	1
TGTCTAGGGAAAAGTAAAAAAAGAAAAACCT	3	39	0
AAAATGACGGCAAGCTAAAAACTTTTG    	2	6	0
GAAAAACAAAAAAGTTGGAAAATGAACTTAC	4	16	0
GTTATTTTAAAAATTTAAAAATA        	8	2	0
TAACCAAGCAAAAGCTTAAATAATTATGAAG	0	40	0
GTTGGGATAGACAGTAGAAAATTTCCTGTTA	6	265	1
TTTGCAGCGCAAAGTATAAATCTCCTTGACG	6	226	1
GTAACGGCATCAATTTGAAAAGAATTCTTTT	3	111	0
         ACCGGTTAAAAATTTCCGGTTA	1	15	0
         TACAGAAGAAAAATGACGGCAA	2	24	0
          ****** ****
MAP Score: 15.9522

Motif 2
ATAATTTCTTCATAATTATTTAAGCTTTTGCTTGGT	0	33	1
AGCATACGGGAGAAAGTTTAAAACCGTAAAAGGAGA	0	84	1
 TTAATTAACCGGAAATTTTTAACCGGT        	1	9	1
AGAAAAATGACGGCAAGCTAAAAACTTTTG      	2	4	0
AAAGAAAAACCTAAACTTTCAAAGCTGGCAGATCTT	3	15	0
AGCAATCAACCGCAATCTTTTAAGCTTTTTCCGTGT	3	176	0
        CCCATACTATATAAATCTATAGCATTTG	5	2	1
TGTAATGCTGCCCAATCCAAAAAGCTCAAGGGCTTC	6	125	0
TATTTTGCAGCGCAAAGTATAAATCTCCTTGACGAT	6	223	1
TGAGATTAAACAAAAGTTAAAAAACTTCCTGGGTTT	9	19	0
TGTTTAATCTCAAAAGATTTAAACCTCTCCGCATGA	9	43	1
          *  **  ** *** **
MAP Score: 13.6536

Motif 3
AAATAATTATGAAGAAATTATACTCCATGCCG	0	22	0
TATAACCAAGCAAAAGCTTAAATAATTATGAA	0	41	0
TAGCATACGGGAGAAAGTTTAAAACCGTAAAA	0	83	1
          CAAAAGTTTTTAGCTTGCCGTC	2	0	1
AGTAAAAAAAGAAAAACCTAAACTTTCAAAGC	3	26	0
CCTGTCTAGGGAAAAGTAAAAAAAGAAAAACC	3	40	0
TGCCGACACGGAAAAAGCTTAAAAGATTGCGG	3	171	1
ATAATCTGCTGAAAAACAAAAAAGTTGGAAAA	4	25	0
AAATTAATTCGAAAAATTATTATGTCGATTAA	4	88	1
AATTTGTGGAGAAAAGGCTATGAGGTGAAAGC	5	52	1
CAGATAACCACAAAAGACTATGTGCTAGTTTA	6	44	1
CTGCCCAATCCAAAAAGCTCAAGGGCTTCCAT	6	122	0
ATTTTGCAGCGCAAAGTATAAATCTCCTTGAC	6	224	1
CAAGTTATTTTAAAAATTTAAAAATA      	8	4	0
TGAGATTAAACAAAAGTTAAAAAACTTCCTGG	9	23	0
TGTTTAATCTCAAAAGATTTAAACCTCTCCGC	9	43	1
          ******  ****
MAP Score: 12.6349

Motif 4
AACTCGGCATGGAGTATAATTTCTTCATAATTAT	0	18	1
CTTTTGCTTGGTTATATCAAGTGCAATAGCATAC	0	57	1
TCCTTTTACGGTTTTAAACTTTCTCCCGTATGCT	0	84	0
       ACCGGTTAAAAATTTCCGGTTAATTAA	1	10	0
AGCCCCACCAGCTAAAAGAATTCTTTTCAAATTG	3	98	1
GCCGTTACTAGCACTAAAGAGTGCAGAACATCAA	3	134	1
CACGGAAAAAGCTTAAAAGATTGCGGTTGATTGC	3	177	1
TTGCGATATTGTTATATAATTTGTGGAGAAAAGG	5	35	1
AATCCAAAAAGCTCAAGGGCTTCCATCATCCTAA	6	114	0
GGATTGGGCAGCATTACAGATTGCAAGCTCTCTC	6	143	1
TCGTCAAGGAGATTTATACTTTGCGCTGCAAAAT	6	224	0
TTAAACAAAAGTTAAAAAACTTCCTGGGTTTTCA	9	16	0
          * * ** ** ****
MAP Score: 6.85895

Motif 5
AATAGCATACGGGAGAAAGTTTAAAACCGTA	0	81	1
      ACCGGTTAAAAATTTCCGGTTAATT	1	12	0
GACGATCTTAGAGAAAGGAATCAGACCAGCC	3	71	1
AGCCCCACCAGCTAAAAGAATTCTTTTCAAA	3	98	1
ACGGAAAAAGCTTAAAAGATTGCGGTTGATT	3	178	1
ATAATTTGTGGAGAAAAGGCTATGAGGTGAA	5	50	1
TTTTACCTTACGGAGAAGATTGACGTGCCCG	6	11	1
AGCAGATAACCACAAAAGACTATGTGCTAGT	6	42	1
CCTGTGAGAGGTGAGAGAGCTTGCAATCTGT	6	158	0
CTCACAGGGACAGAGAAGAATGGTGCAGCTC	6	181	1
AAAATTTCCTGTTAAAGGGTTCTTTTCT   	6	282	1
TTAAACAAAAGTTAAAAAACTTCCTGGGTTT	9	19	0
TTTGTTTAATCTCAAAAGATTTAAACCTCTC	9	41	1
TCCCGTCATGCGGAGAGGTTTAAATCTTTTG	9	53	0
          * *********
MAP Score: 6.06952

Motif 6
ATAGCATACGGGAGAAAGTTTAAAACCGTA	0	82	1
AACCGTAAAAGGAGAGGAGGT         	0	105	1
TATAATTTGTGGAGAAAAGGCTATGAGGTG	5	49	1
TTTACCTTACGGAGAAGATTGACGTGCCCG	6	12	1
GGGATAGACAGTAGAAAATTTCCTGTTAAA	6	268	1
CCCGTCATGCGGAGAGGTTTAAATCTTTTG	9	53	0
          **********
MAP Score: 2.2787

Motif 7
       ACCAGTAGAACTCGGCATGGAGTATAATTTCT	0	3	1
         CAAAAGTTTTTAGCTTGCCGTCATTTTTCT	2	1	1
CCGCAATCTTTTAAGCTTTTTCCGTGTCGGCAGCGTTGA	3	164	0
TTGAGCTTTTTGGATTGGGCAGCATTACAGATTGCAAGC	6	132	1
GGGACAGAGAAGAATGGTGCAGCTCTCCGTCGCCTATAT	6	187	1
TGCAGCGCAAAGTATAAATCTCCTTGACGATCCTCTGGT	6	228	1
      CCGTTATAAGTTGCACCGTTGCGCAACCAAACA	7	4	1
TCAAAAGATTTAAACCTCTCCGCATGACGGGATTGT   	9	52	1
          *  *    ** ** ** **
MAP Score: 1.01376