AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_operons010_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242609
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF0106	116	aspartate carbamoyltransferase, catalytic subunit (pyrB)
#1	AF0252	251	CTP synthase (pyrG)
#2	AF1240	81	tryptophan synthase, subunit beta (trpB-1)
#3	AF1255	27	ornithine carbamoyltransferase (argF)
#4	AF1259	36	inosine monophosphate dehydrogenase, putative
#5	AF1260	207	phosphoribosylformylglycinamidine synthase I (purQ)
#6	AF1261	133	medium-chain acyl-CoA ligase (alkK-4)
#7	AF1263	74	iron-sulfur cluster binding protein
#8	AF1269	300	A. fulgidus predicted coding region AF1269
#9	AF1270	33	transcriptional regulatory protein, ArsR family
#10	AF1316	48	threonine synthase (thrC-2)
#11	AF1319	300	A. fulgidus predicted coding region AF1319
#12	AF1320	24	GMP synthase (guaA-2)
#13	AF1342	126	thymidine phosphorylase (deoA-2)
#14	AF1604	300	anthranilate synthase component II (trpD)
#15	AF2251	30	competence-damage protein, putative
#16	AF2252	78	argininosuccinate synthetase (argG)

Motif 1
CCTTTTACGGTTTTAAACTTTCTCCCGTATG	0	86	0
AACCGCAATCTTTTAAGCTTTTTCCGTGTCG	5	174	0
CCCAGGAAGTTTTTTAACTTTTGTTTAATCT	16	22	1
CGCGAAGTGTATTTAAGCTTTTTGCTATAGT	14	253	0
CTTCATAATTATTTAAGCTTTTGCTTGGTTA	0	40	1
GCTAAATAAATTTTAATCTTGGACTGGAGTC	11	183	1
    CAAAAGTTTTTAGCTTGCCGTCATTTT	4	6	1
AGGTTTTTCTTTTTTTACTTTTCCCTAGACA	5	39	1
       TATTTTTAAATTTTTAAAATAACT	15	3	1
          TTTTTACCTTACGGAGAAGAT	8	0	1
AATATAACCATTTTTAACTTAGCTGGAATTG	11	225	0
CGTCAAGGAGATTTATACTTTGCGCTGCAAA	8	226	0
TGCGGAGAGGTTTAAATCTTTTGAGATTAAA	16	45	0
   TCATTTTATTTAAGTTTTTTCCCATTAA	2	63	0
ATTTTCCAACTTTTTTGTTTTTCAGCAGATT	6	24	1
AAATGGTTATATTTATTTTTTATCCTCAAAA	11	243	1
          ****** ****
MAP Score: 19.0873

Motif 2
GCAATCTTTTAAGCTTTTTCCGTGTCGGCA	5	171	0
GTGTGAACCAAAGCTTCTTCATCAGGTCTT	14	47	0
AAGTGTATTTAAGCTTTTTGCTATAGTATG	14	250	0
TTACGGTTTTAAACTTTCTCCCGTATGCTA	0	83	0
AAAGTCACCTAAACTTTCTGATAAGAGATG	14	206	0
AAAAGTTAAAAAACTTCCTGGGTTTTCAGA	16	14	0
GAAAGAATATTAACTTTTTCTCGCTATCGT	13	89	0
ACATTATCTATAACTTCTTCACGATAGCGA	13	69	1
GTCAGCTTTAAAACCTTTTCAGGTGAGAAT	13	24	1
CATTTTATTTAAGTTTTTTCCCATTAAATG	2	60	0
ATAATTATTTAAGCTTTTGCTTGGTTATAT	0	44	1
CATGAAAAGGAAGCTTCTGGAAATCCTCGC	1	81	1
AGACAGTAGAAAATTTCCTGTTAAAGGGTT	8	273	1
     GGTTAAAACTTGTTGGTGAATTAAA	11	285	0
GGAAGCCCTTGAGCTTTTTGGATTGGGCAG	8	124	1
TTTCACCTCATAGCCTTTTCTCCACAAATT	7	52	0
GCATGGAGTATAATTTCTTCATAATTATTT	0	24	1
TAAATAAAGGTAATTTTTTGAGGATAAAAA	11	259	0
GGAGAGGTTTAAATCTTTTGAGATTAAACA	16	43	0
 ACCGGTTAAAAATTTCCGGTTAATTAA  	3	8	0
AACTAGCACATAGTCTTTTGTGGTTATCTG	8	44	0
TTTCCAGATATAATCTCCTCTTCGTTCTCC	1	153	0
          **********
MAP Score: 18.6737

Motif 3
CAATTCCGACTTGCAGAGAGGACACGCGAG	1	106	0
GTTGAAGTGGTTGAGGAGAACGAAGAGGAG	1	139	1
GAATTTCCCATTGAGGATGGGATTCCAGAT	1	208	1
AAATGTTTTCTTGCTGAGAATGTTCCCATT	2	34	1
GGTTAAAAATTTCCGGTTAATTAA      	3	4	0
GCTTAAAAGATTGCGGTTGATTGCTTACCG	5	187	1
GTTATATAATTTGTGGAGAAAAGGCTATGA	7	45	1
AGAAAAGGCTATGAGGTGAAAGC       	7	61	1
  TTTTTACCTTACGGAGAAGATTGACGTG	8	8	1
AGTAGAAAATTTCCTGTTAAAGGGTTCTTT	8	277	1
CCTTTATCGTTTCTGGATAGTTAACGATGG	11	29	1
AGGTAATTTTTTGAGGATAAAAAATAAATA	11	252	0
TTAAAACCTTTTCAGGTGAGAATTTTTAAA	13	31	1
AATCTCATGATTGAGGTTAAGGCCAGCACA	14	112	1
CAATCCCGTCATGCGGAGAGGTTTAAATCT	16	57	0
          **********
MAP Score: 9.39665

Motif 4
AATGCTGTTGGAGGTATGAGTAAATAACGA	1	51	0
GTCGGAATTGGAAGTTGAAGTGGTTGAGGA	1	126	1
TGAAGTGGTTGAGGAGAACGAAGAGGAGAT	1	141	1
ATTTCCCATTGAGGATGGGATTCCAGATTT	1	210	1
AAAAGGCTATGAGGTGAAAGC         	7	63	1
CCTTAGTTAGGATGATGGAAGCCCTTGAGC	8	108	1
GTCCCTGTGAGAGGTGAGAGAGCTTGCAAT	8	162	0
GAACACTCCAGATGTAAGAAGTTCAGGAAT	11	77	0
GTAATTTTTTGAGGATAAAAAATAAATATA	11	250	0
CCGAAGACCTGATGAAGAAGCTTTGGTTCA	14	44	1
TCATCCAGCTGAGGTGTGAACCAAAGCTTC	14	60	0
ACCTCAGCTGGATGAAGAAGCGAGGAGGAA	14	75	1
ATGAAGAAGCGAGGAGGAAGATAGAAAATC	14	86	1
TCTCATGATTGAGGTTAAGGCCAGCACAGT	14	114	1
TGGCAAAAAAGAGGTAAAAGTCACCTAAAC	14	222	0
GTCATGCGGAGAGGTTTAAATCTTTTGAGA	16	50	0
          **********
MAP Score: 9.14652

Motif 5
CGGCATGGAGTATAATTTCTTCATAATTATTTAAGCTT	0	22	1
TTCCAGAAGCTTCCTTTTCATGAATGCTGTTGGAGGTA	1	65	0
AATCCTCGCGTGTCCTCTCTGCAAGTCGGAATTGGAAG	1	102	1
GCTTTCCAGATATAATCTCCTCTTCGTTCTCCTCAACC	1	147	0
          TTAATTAACCGGAAATTTTTAACCGGT 	3	0	1
CAAAAGTTTTTAGCTTGCCGTCATTTTTCTTCTGTA  	4	10	1
TTTAAGCTTTTTCCGTGTCGGCAGCGTTGATGTTCTGC	5	156	0
TAACTGAAAATAAACTTTCAGGATTCTTAAGTAAATTA	6	56	1
CTGATACCTTTATCGTTTCTGGATAGTTAACGATGGGG	11	23	1
AATATTAATATAGAATTCCTGAACTTCTTACATCTGGA	11	63	1
CTTATTAAATTGCAATTCCAGCTAAGTTAAAAATGGTT	11	213	1
     GATGTTAAATTGTCGTCAGCTTTAAAACCTTTT	13	5	1
ACCCGGCAGTTTACGTTCCCGAAGACCTGATGAAGAAG	14	26	1
TGCACCGACCTCAAATCCCGGAATGCCTCCTTCAGGCT	14	146	0
CGGTGGATCATCTCTTATCAGAAAGTTTAGGTGACTTT	14	198	1
    AACCTCTGAAAACCCAGGAAGTTTTTTAACTTTT	16	6	1
          *  * * ** ***   **
MAP Score: 7.841

Motif 6
TACCTCCAACAGCATTCATGAAAAGGAAGCT	1	65	1
GGACACGCGAGGATTTCCAGAAGCTTCCTTT	1	86	0
GCTGCAAACGAGCTTTCCAGATATAATCTCC	1	165	0
CATTGAGGATGGGATTCCAGATTTGCGCCCT	1	216	1
TGGATTGGGCAGCATTACAGATTGCAAGCTC	8	142	1
    TAATATGGAATTGCTGATACCTTTATC	11	6	1
ATATTAATATAGAATTCCTGAACTTCTTACA	11	64	1
GCCTCCTTCAGGCTTTACTGTGCTGGCCTTA	14	129	0
GCCTGAAGGAGGCATTCCGGGATTTGAGGTC	14	147	1
AAAACTTCCTGGGTTTTCAGAGGTT      	16	4	0
          ******** **
MAP Score: 6.19006

Motif 7
TCCTCAACCACTTCAACTTCCAATTCCGACT	1	125	0
ATAATCTCCTCTTCGTTCTCCTCAACCACTT	1	143	0
GATTCCAGATTTGCGCCCTCCGGAGTTGAGA	1	228	1
         GCTTCGCTCTCTCCAATTCGTT	2	1	1
ATCTGTAATGCTGCCCAATCCAAAAAGCTCA	8	133	0
CTGCACCATTCTTCTCTGTCCCTGTGAGAGG	8	178	0
    TTTTTCCTTCACCAACTTAAGGGC   	12	6	1
TGAACCAAAGCTTCTTCATCAGGTCTTCGGG	14	43	0
TTCCTCCTCGCTTCTTCATCCAGCTGAGGTG	14	74	0
GATTTTCTATCTTCCTCCTCGCTTCTTCATC	14	85	0
GCCGTTAAGGCTGCACCGACCTCAAATCCCG	14	164	0
          CTGCTCCCACCATGTGGGATT	14	289	0
          **** ******
MAP Score: 4.95509