AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_fusions018_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241554
 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	AF1269	300	A. fulgidus predicted coding region AF1269
#5	AF1270	33	transcriptional regulatory protein, ArsR family
#6	AF2251	30	competence-damage protein, putative
#7	AF2252	78	argininosuccinate synthetase (argG)

Motif 1
TTCATAATTATTTAAGCTTTTGCTTGGTTA	0	41	1
ACCGCAATCTTTTAAGCTTTTTCCGTGTCG	3	174	0
CCAGGAAGTTTTTTAACTTTTGTTTAATCT	7	23	1
CTTTTACGGTTTTAAACTTTCTCCCGTATG	0	86	0
   CAAAAGTTTTTAGCTTGCCGTCATTTT	2	7	1
GGTTTTTCTTTTTTTACTTTTCCCTAGACA	3	40	1
GTCAAGGAGATTTATACTTTGCGCTGCAAA	4	226	0
AAAAGAATTCTTTTAGCTGGTGGGGCTGGT	3	95	0
       TATTTTTAAATTTTTAAAATAAC	6	3	1
          TTTTTACCTTACGGAGAAGA	4	0	1
AACAGGAAATTTTCTACTGTCTATCCCAAC	4	265	0
AACCGGAAATTTTTAACCGGT         	1	16	1
AAAGAATTCTTTTCAAATTGATGCCGTTAC	3	112	1
          **********
MAP Score: 17.9609

Motif 2
   ACCAGTAGAACTCGGCATGGAGTATAATTTCTTCAT	0	7	1
GCACGTCAATCTTCTCCGTAAGGTAAAAA          	4	0	0
TTGTGGTTATCTGCTCGGGCACGTCAATCTTCTCCGTAA	4	18	0
CTAGTTTATGGTGCTCTGTACGGTCTGAATAAACAAAGA	4	68	1
CAAGCTCTCTCACCTCTCACAGGGACAGAGAAGAATGGT	4	166	1
AAGAATGGTGCAGCTCTCCGTCGCCTATATTTTGCAGCG	4	196	1
CTCCTTGACGATCCTCTGGTTGGGATAGACAGTAGAAAA	4	247	1
          ** *** *   **   * *
MAP Score: 4.20756

Motif 3
ATTTCTTCATAATTATTTAAGCTTTTGCTTGGT	0	36	1
CATACGGGAGAAAGTTTAAAACCGTAAAAGGAG	0	86	1
AATTAACCGGAAATTTTTAACCGGT        	1	12	1
        CAAAAGTTTTTAGCTTGCCGTCATT	2	2	1
GAAAAACCTAAACTTTCAAAGCTGGCAGATCTT	3	15	0
GAAAAGTAAAAAAAGAAAAACCTAAACTTTCAA	3	29	0
ATTTGAAAAGAATTCTTTTAGCTGGTGGGGCTG	3	97	0
AATCAACCGCAATCTTTTAAGCTTTTTCCGTGT	3	176	0
AATGCTGCCCAATCCAAAAAGCTCAAGGGCTTC	4	125	0
TTTGCAGCGCAAAGTATAAATCTCCTTGACGAT	4	226	1
AGTTATTTTAAAAATTTAAAAATA         	6	1	0
AAAACCCAGGAAGTTTTTTAACTTTTGTTTAAT	7	18	1
ACTTTTGTTTAATCTCAAAAGATTTAAACCTCT	7	38	1
          **  ****** **
MAP Score: 2.97022

Motif 4
TGGTTATATCAAGTGCAATAGCATACGGGAGAAAGTTTA	0	65	1
ATACGGGAGAAAGTTTAAAACCGTAAAAGGAGAGGAGGT	0	87	1
    TTAATTAACCGGAAATTTTTAACCGGT        	1	6	1
TAAAAAAAGAAAAACCTAAACTTTCAAAGCTGGCAGATC	3	17	0
ACGCTGCCGACACGGAAAAAGCTTAAAAGATTGCGGTTG	3	167	1
CCGAGCAGATAACCACAAAAGACTATGTGCTAGTTTATG	4	39	1
GTACGGTCTGAATAAACAAAGAACCTTAGTTAGGATGAT	4	85	1
AATGCTGCCCAATCCAAAAAGCTCAAGGGCTTCCATCAT	4	119	0
  TATTTTTAAATTTTTAAAATAACTTGGAAC       	6	8	1
GATTAAACAAAAGTTAAAAAACTTCCTGGGTTTTCAGAG	7	13	0
TTTAATCTCAAAAGATTTAAACCTCTCCGCATGACGGGA	7	45	1
          **    **** * **   *
MAP Score: 0.830534

Motif 5
TGGTTATATCAAGTGCAATAGCATACGGGAGAAAGTTTA	0	65	1
GAAAGTTTAAAACCGTAAAAGGAGAGGAGGT        	0	95	1
        CAAAAGTTTTTAGCTTGCCGTCATTTTTCTT	2	2	1
GAAAAACCTAAACTTTCAAAGCTGGCAGATCTTTAATT 	3	9	0
ATTTGAAAAGAATTCTTTTAGCTGGTGGGGCTGGTCTGA	3	91	0
ACGCTGCCGACACGGAAAAAGCTTAAAAGATTGCGGTTG	3	167	1
AGGATGATGGAAGCCCTTGAGCTTTTTGGATTGGGCAGC	4	116	1
TTGGATTGGGCAGCATTACAGATTGCAAGCTCTCTCACC	4	141	1
TCACCTCTCACAGGGACAGAGAAGAATGGTGCAGCTCTC	4	175	1
GATTAAACAAAAGTTAAAAAACTTCCTGGGTTTTCAGAG	7	13	0
ACAATCCCGTCATGCGGAGAGGTTTAAATCTTTTGAGAT	7	49	0
          **     * *****   **
MAP Score: 0.716416

Motif 6
ATATAACCAAGCAAAAGCTTAAATAATTATG	0	43	0
TAGCATACGGGAGAAAGTTTAAAACCGTAAA	0	83	1
TCTGCCAGCTTTGAAAGTTTAGGTTTTTCTT	3	19	1
TCCCTAGACAGGACGATCTTAGAGAAAGGAA	3	60	1
TGCCGACACGGAAAAAGCTTAAAAGATTGCG	3	171	1
TGTGAGAGGTGAGAGAGCTTGCAATCTGTAA	4	156	0
          * *********
MAP Score: 0.301193