AlignACE 3.0 10/20/99
AlignACE2 -i PA/PA_operons026_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944250237
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PAB0562	300	hypothetical protein
#1	PAB0563	41	PAB0563
#2	PAB1455	81	hypothetical protein
#3	PAB1379	67	PAB1379
#4	PAB1378	115	PAB1378
#5	PAB1376	141	hypothetical protein

Motif 1
AAAACTTGACTTCGTTGAGGCGCTAGTTCTGG	0	33	1
AATAGCTTAATTTTCTCGACCGAAAAGCTTAT	0	146	1
CAGCCCGATGTTTGATGGGAGGGGAATTGTTT	0	178	0
CAAACATCGGGCTGTGGGCCGGTAGCTTAGCC	0	196	1
CTTAGCCTGGTTAGAGCGGCGGACTCTTAATC	0	221	1
CTCTTAATCCGCAGGTCGGGGGTTCAAATCCC	0	244	1
GAAGAGTCTGGCGGGCCGGGGGGGATTTGAAC	0	265	0
CCCGCCAGACTCTTCTCAGGGGAGAAAA    	0	282	1
CAATTAAACATTGGGTGACGGG          	1	29	1
ACCTTTTAAATCCTTTGGAGGGAAAAGACC  	2	8	0
ATTAGCAAATTCCTATCGCAGGTAATCCCGAT	2	56	1
TAACATTAATTTCTTTGAGGGGTGATACT   	3	48	1
          ** * *******
MAP Score: 7.81184

Motif 2
CGAAGTCAAGTTTTAACACTTTTCTTGCAAGA	0	15	0
AATAGCTTAATTTTCTCGACCGAAAAGCTTAT	0	146	1
CCGGGGGGGATTTGAACCCCCGACCTGCGGAT	0	250	0
          TTTTCTCCCCTGAGAAGAGTCT	0	288	0
      GGTCTTTTCCCTCCAAAGGATTTAAA	2	4	1
TTTCCAAACCTTTTAAATCCTTTGGAGGGAAA	2	15	0
ATAAGATTTATTTTCCAAACCTTTTAAATCCT	2	26	0
AACCTTGCCTTTTTACCTCTCTTTCGATTTTA	3	18	1
CAAAAAATGGTTTTATATCCAGCCATTTTTAG	4	87	1
TTTGGACCTTTTTTACCCCTATATAATAATGC	5	108	0
          ******* ** *
MAP Score: 6.00443

Motif 3
TTAATGTCTACAGGCTCCAAAGGTTCCAGA	0	60	0
TGCCTCTTCACGGACTCCTCAATCTTAATG	0	84	0
AGCGTATCCTCTGCCTCTTCACGGACTCCT	0	95	0
GTTAGAGCGGCGGACTCTTAATCCGCAGGT	0	230	1
CCCGGCCCGCCAGACTCTTCTCAGGGGAGA	0	277	1
TCAACTTTTACAGGCACTTCCACACACAAA	4	61	1
          **********
MAP Score: 5.55625

Motif 4
GAAGAGTCTGGCGGGCCGGGGGGGATTTGAAC	0	265	0
CAGCCCGATGTTTGATGGGAGGGGAATTGTTT	0	178	0
CTCTTAATCCGCAGGTCGGGGGTTCAAATCCC	0	244	1
CTTAGCCTGGTTAGAGCGGCGGACTCTTAATC	0	221	1
CATTAATTTCTTTGAGGGGTGATACT      	3	51	1
ACATCGGGCTGTGGGCCGGTAGCTTAGCCTGG	0	199	1
TTTTAAATCCTTTGGAGGGAAAAGACC     	2	5	0
GCCAGACTCTTCTCAGGGGAGAAAA       	0	285	1
GTAGTTGAATTTTTAAGGGAGATCGGA     	5	5	0
          ***** *** **
MAP Score: 5.06123

Motif 5
TTGCAAGAAAAGTGTTAAAACTTGACTTCG	0	17	1
CCGCAGGTCGGGGGTTCAAATCCCCCCCGG	0	252	1
GACTCTTCTCAGGGGAGAAAA         	0	289	1
AAATCGAAAGAGAGGTAAAAAGGCAAGGTT	3	18	0
AATTTCTTTGAGGGGTGATACT        	3	55	1
ATTATTATATAGGGGTAAAAAAGGTCCAAA	5	110	1
AGGGGTAAAAAAGGTCCAAAGGTGATGCCC	5	120	1
          **********
MAP Score: 2.1129

Motif 6
CTCTTCACGGACTCCTCAATCTTAATGTCTACAGGC	0	75	0
AGCTTAATTTTCTCGACCGAAAAGCTTATAAACAAT	0	149	1
TATAAACAATTCCCCTCCCATCAAACATCGGGCTGT	0	175	1
GGATTTGAACCCCCGACCTGCGGATTAAGAGTCCGC	0	239	0
GGGGTTCAAATCCCCCCCGGCCCGCCAGACTCTTCT	0	262	1
     TTTTCTCCCCTGAGAAGAGTCTGGCGGGCCG	0	279	0
    GGTCTTTTCCCTCCAAAGGATTTAAAAGGTTT	2	6	1
    AGTATCACCCCTCAAAGAAATTAATGTTAAAA	3	45	0
TACAGGCACTTCCACACACAAAAAATGGTTTTATAT	4	69	1
TAAAAATTCAACTACGCCCATGTATTTAAGGTTTCT	5	22	1
TTGGACCTTTTTTACCCCTATATAATAATGCATGCA	5	103	0
          ***** ** *   * *
MAP Score: 0.44889

Motif 7
CTTGACTTCGTTGAGGCGCTAGTTCTGGAAC	0	37	1
AGCCCGATGTTTGATGGGAGGGGAATTGTTT	0	178	0
AAACATCGGGCTGTGGGCCGGTAGCTTAGCC	0	197	1
TTAGCCTGGTTAGAGCGGCGGACTCTTAATC	0	222	1
GAGAAGAGTCTGGCGGGCCGGGGGGGATTTG	0	268	0
CAATTAAACATTGGGTGACGGG         	1	29	1
ATTAATTTCTTTGAGGGGTGATACT      	3	52	1
          *** *******
MAP Score: 0.17505