AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_operons010_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242587
 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	AF1269	300	A. fulgidus predicted coding region AF1269
#7	AF1270	33	transcriptional regulatory protein, ArsR family
#8	AF1316	48	threonine synthase (thrC-2)
#9	AF1319	300	A. fulgidus predicted coding region AF1319
#10	AF1320	24	GMP synthase (guaA-2)
#11	AF1342	126	thymidine phosphorylase (deoA-2)
#12	AF1604	300	anthranilate synthase component II (trpD)
#13	AF2251	30	competence-damage protein, putative
#14	AF2252	78	argininosuccinate synthetase (argG)

Motif 1
AAGTGTATTTAAGCTTTTTGCTATAGTATG	12	250	0
GCAATCTTTTAAGCTTTTTCCGTGTCGGCA	5	171	0
GTGTGAACCAAAGCTTCTTCATCAGGTCTT	12	47	0
AAAGTCACCTAAACTTTCTGATAAGAGATG	12	206	0
AAAAGTTAAAAAACTTCCTGGGTTTTCAGA	14	14	0
TTACGGTTTTAAACTTTCTCCCGTATGCTA	0	83	0
CATGAAAAGGAAGCTTCTGGAAATCCTCGC	1	81	1
GAAAGAATATTAACTTTTTCTCGCTATCGT	11	89	0
CATTTTATTTAAGTTTTTTCCCATTAAATG	2	60	0
ACATTATCTATAACTTCTTCACGATAGCGA	11	69	1
ATAATTATTTAAGCTTTTGCTTGGTTATAT	0	44	1
GTCAGCTTTAAAACCTTTTCAGGTGAGAAT	11	24	1
AGACAGTAGAAAATTTCCTGTTAAAGGGTT	6	273	1
     GGTTAAAACTTGTTGGTGAATTAAA	9	285	0
GGAAGCCCTTGAGCTTTTTGGATTGGGCAG	6	124	1
TAAATAAAGGTAATTTTTTGAGGATAAAAA	9	259	0
GGAGAGGTTTAAATCTTTTGAGATTAAACA	14	43	0
GCATGGAGTATAATTTCTTCATAATTATTT	0	24	1
 ACCGGTTAAAAATTTCCGGTTAATTAA  	3	8	0
AACTAGCACATAGTCTTTTGTGGTTATCTG	6	44	0
TTTCCAGATATAATCTCCTCTTCGTTCTCC	1	153	0
          **********
MAP Score: 18.5533

Motif 2
ATACGGGAGAAAGTTTAAAACCGTAAAAGG	0	87	1
GATTAAACAAAAGTTAAAAAACTTCCTGGG	14	22	0
AATTCCAGCTAAGTTAAAAATGGTTATATT	9	226	1
GACACGGAAAAAGCTTAAAAGATTGCGGTT	5	175	1
AAATGACGGCAAGCTAAAAACTTTTG    	4	6	0
AACCAAGCAAAAGCTTAAATAATTATGAAG	0	40	0
CTATAGCAAAAAGCTTAAATACACTTCGCG	12	254	1
ACTCCAGTCCAAGATTAAAATTTATTTAGC	9	183	0
TCTTCTCCGTAAGGTAAAAA          	6	0	0
TCATGCGGAGAGGTTTAAATCTTTTGAGAT	14	49	0
AATGTTGTTTATGTTTAAAAATTCTCACCT	11	44	0
TTATTTTAAAAATTTAAAAATA        	13	2	0
GTCTAGGGAAAAGTAAAAAAAGAAAAACCT	5	39	0
TAATTTTTTGAGGATAAAAAATAAATATAA	9	249	0
TTTCCGCCTTAATTTTAAATACCGCAAAAA	1	21	0
TTGCAGCGCAAAGTATAAATCTCCTTGACG	6	227	1
          **********
MAP Score: 18.4408

Motif 3
   ACCAGTAGAACTCGGCATGGAGTATAATTT	0	7	1
CCTCGCGTGTCCTCTCTGCAAGTCGGAATTGGA	1	105	1
     TGTCTCAACTCCGGAGGGCGCAAATCTG	1	233	0
AAATGGGAACATTCTCAGCAAGAAAACATTTAA	2	32	0
GCACGTCAATCTTCTCCGTAAGGTAAAAA    	6	6	0
GTCTTTTGTGGTTATCTGCTCGGGCACGTCAAT	6	29	0
CTAGTTTATGGTGCTCTGTACGGTCTGAATAAA	6	68	1
CTCCTTGACGATCCTCTGGTTGGGATAGACAGT	6	247	1
CATGGAAATACCACTCAGTTCGGGTAATGTGAA	9	104	0
CTTTGGTTCACACCTCAGCTGGATGAAGAAGCG	12	64	1
AAGATTTAAACCTCTCCGCATGACGGGATTGT 	14	56	1
          ** *** *** **
MAP Score: 9.15066

Motif 4
AAAACCGTAAAAGGAGAGGAGGT       	0	103	1
ATTCCGACTTGCAGAGAGGACACGCGAGGA	1	104	0
GTTGAGGAGAACGAAGAGGAGATTATATCT	1	148	1
TTTTTACCTTACGGAGAAGATTGACGTGCC	6	10	1
TCTCACAGGGACAGAGAAGAATGGTGCAGC	6	180	1
AATATAGGCGACGGAGAGCTGCACCATTCT	6	197	0
GGATGAAGAAGCGAGGAGGAAGATAGAAAA	12	84	1
TAGTATGGCAAAAAAGAGGTAAAAGTCACC	12	227	0
ATCCCGTCATGCGGAGAGGTTTAAATCTTT	14	55	0
          **********
MAP Score: 8.29472

Motif 5
TCTCCTTTTACGGTTTTAAACTTTCTCCCGTATGCTATTG	0	80	0
         GCTGGTAGGCTTTTTTGCGGTATTTAAAATT	1	1	1
GAAAAGGAAGCTTCTGGAAATCCTCGCGTGTCCTCTCTGC	1	84	1
TCGGAATTGGAAGTTGAAGTGGTTGAGGAGAACGAAGAGG	1	127	1
CTGGAAAGCTCGTTTGCAGCAGTTGTCGTGCTGAATTTCC	1	176	1
GATGGGATTCCAGATTTGCGCCCTCCGGAGTTGAGACA  	1	223	1
         ACCGGTTAAAAATTTCCGGTTAATTAA    	3	6	0
AAAGATCTGCCAGCTTTGAAAGTTTAGGTTTTTCTTTTTT	5	14	1
GGCAGCGTTGATGTTCTGCACTCTTTAGTGCTAGTAACGG	5	135	0
GACACGGAAAAAGCTTAAAAGATTGCGGTTGATTGCTTAC	5	175	1
ACCACAAAAGACTATGTGCTAGTTTATGGTGCTCTGTACG	6	50	1
CTTAGTTAGGATGATGGAAGCCCTTGAGCTTTTTGGATTG	6	109	1
AAATTGTCGTCAGCTTTAAAACCTTTTCAGGTGAGAATTT	11	16	1
ACTCTGAAAGAATATTAACTTTTTCTCGCTATCGTGAAGA	11	84	0
TCCCGAAGACCTGATGAAGAAGCTTTGGTTCACACCTCAG	12	42	1
AGCGAGGAGGAAGATAGAAAATCTCATGATTGAGGTTAAG	12	93	1
GAGGTCGGTGCAGCCTTAACGGCTCTCGGTGGATCATCTC	12	172	1
TGGATCATCTCTTATCAGAAAGTTTAGGTGACTTTTACCT	12	201	1
GATTAAACAAAAGTTAAAAAACTTCCTGGGTTTTCAGAGG	14	12	0
TCATGCGGAGAGGTTTAAATCTTTTGAGATTAAACAAAAG	14	39	0
          * * *  **   ***  * *
MAP Score: 6.64827

Motif 6
CTTCAACTTCCAATTCCGACTTGCAGAGAGGACACGCGAGG	1	105	0
AGGAATCAGACCAGCCCCACCAGCTAAAAGAATTCTTTTCA	5	86	1
ATTGACGTGCCCGAGCAGATAACCACAAAAGACTATGTGCT	6	29	1
TTTATTCAGACCGTACAGAGCACCATAAACTAGCACATAGT	6	60	0
AGCTCTCTCACCTCTCACAGGGACAGAGAAGAATGGTGCAG	6	168	1
ACTGTCTATCCCAACCAGAGGATCGTCAAGGAGATTTATAC	6	239	0
AGGTTAAGGCCAGCACAGTAAAGCCTGAAGGAGGCATTCCG	12	125	1
TAAGGCTGCACCGACCTCAAATCCCGGAATGCCTCCTTCAG	12	149	0
          AACCTCTGAAAACCCAGGAAGTTTTTTAACT	14	0	1
         ACAATCCCGTCATGCGGAGAGGTTTAAATCTT	14	56	0
          **   * **    *  *** *
MAP Score: 4.61514

Motif 7
CCTCGCGTGTCCTCTCTGCAAGTCGGAATTGGAAGTTGAAG	1	105	1
     TGTCTCAACTCCGGAGGGCGCAAATCTGGAATCCCA	1	225	0
     AATTAAAGATCTGCCAGCTTTGAAAGTTTAGGTTTT	5	5	1
ATTGACGTGCCCGAGCAGATAACCACAAAAGACTATGTGCT	6	29	1
AGCTCTCTCACCTCTCACAGGGACAGAGAAGAATGGTGCAG	6	168	1
ACTGTCTATCCCAACCAGAGGATCGTCAAGGAGATTTATAC	6	239	0
CTTTGGTTCACACCTCAGCTGGATGAAGAAGCGAGGAGGAA	12	64	1
AGGTTAAGGCCAGCACAGTAAAGCCTGAAGGAGGCATTCCG	12	125	1
ATAAGAGATGATCCACCGAGAGCCGTTAAGGCTGCACCGAC	12	175	0
          AACCTCTGAAAACCCAGGAAGTTTTTTAACT	14	0	1
AAGATTTAAACCTCTCCGCATGACGGGATTGT         	14	56	1
          ** * * *   * *   ** *
MAP Score: 4.51285

Motif 8
ATAGCATACGGGAGAAAGTTTAAAACCGTAAAAG	0	82	1
CCATTTAATGGGAAAAAACTTAAATAAAATGA  	2	59	1
CTGCCGACACGGAAAAAGCTTAAAAGATTGCGGT	5	170	1
ATTCTCACCTGAAAAGGTTTTAAAGCTGACGACA	11	20	0
CCTTTTCAGGTGAGAATTTTTAAACATAAACAAC	11	37	1
TAATATTCTTTCAGAGTTTTTGAAGTTCA     	11	107	1
CCATACTATAGCAAAAAGCTTAAATACACTTCGC	12	249	1
     TATTTTTAAATTTTTAAAATAACTTGGAA	13	5	1
TTGTTTAATCTCAAAAGATTTAAACCTCTCCGCA	14	42	1
          * ***   ******
MAP Score: 3.95798