AlignACE 3.0 10/20/99
AlignACE2 -i PA/PA_profile003_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944251370
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PAB0085	251	hypothetical protein
#1	leuA-2	257	PAB0286
#2	PAB1936	49	PAB1936
#3	apbA	56	PAB0512
#4	PAB0703	82	PAB0703
#5	PAB0780	300	hypothetical protein
#6	graD-3	77	PAB0784
#7	PAB1498	90	PAB1498

Motif 1
CAATAAAATTGAAGGAAGAAGAAAGGAGATCT	0	30	0
GGACATTAATAAACGCTGAGGTTTACATAGGA	1	64	0
GCACATTGAGAAAAGTTGAGGACATTAATAAA	1	83	0
AGGAAGAGGAGAAGGTTAAGGAGAGGCTTAGA	5	23	0
TTTTCACAGAGGAGGAAGAGGAGAAGGTTAAG	5	35	0
AGGAGGAAGAGGAGGAAGAGGTTTTCACAGAG	5	56	0
TAGCAAGCTTGGAGGAGGAAGAGGAGGAAGAG	5	68	0
TTACATACTCAGAGACGGAGGAAAATCCAGTA	5	121	1
CGCTTTACGAGAAGATAGAGAACAGGATCAAG	5	155	0
GGATGAAGATGGGAGATGAGGAGAAGTTTGTA	5	206	0
AGAGGGAAGTGGGGGATGAAGATGGGAGATGA	5	219	0
GCCATTAATAAAAGAGGGAAGTGGGGGATGAA	5	231	0
          *****  *****
MAP Score: 16.3925

Motif 2
AAAGAGACATTTTTCCATAACTTTTTAGCATTACT	0	117	0
ATTCATCTAATATTCCGAAAATTTTATATAGGGTA	1	192	1
TCATCGAAATTATTCTTAAAATTTTATCAGTTTTG	1	158	0
TCCTTGATCCTGTTCTCTATCTTCTCGTAAAGCGT	5	153	1
TCTCCTTTCTTCTTCCTTCAATTTTATTGCTTATA	0	33	1
      TTTCTTTTCCCACTTTTCTCAGATCTCCT	0	4	1
GCTCTAAGCCTCTCCTTAACCTTCTCCTCTTCCTC	5	21	1
TGTGAAAACCTCTTCCTCCTCTTCCTCCTCCAAGC	5	59	1
CGTTTATTAATGTCCTCAACTTTTCTCAATGTGCG	1	81	1
GTTAAGCTTTTATTACAAAATTTCCCTTACTAAAA	6	39	1
TGTCTCTTTTTATTTTTAAGTTTTCATGTATAATT	0	143	1
TGTGCGAAAATTTTTTCTATATTTCTCGAATTTTG	1	110	1
GGTTTTTATATTTCATCGATGTTCTTTAGCTG   	2	7	0
TCTAGCCAAATATTTCCCAAATTTATAAGTTATAA	0	63	0
TCTCTGAGTATGTAACTTATGTTTTGAGGGAGGTC	5	101	0
CTTGCCAATATATCATGGCATTTTTAAATAAGGTA	0	181	0
TTGGCTAGATTATTATAAAACTTTAAGTAGTAATG	0	89	1
 GCCTTCCTGTTTATTAGAATTTTTAACATTTTAG	5	276	0
TAAAGGTTTATATACCCAAGCTTCATCAGTGTGGA	7	57	1
GGATACTGGATTTTCCTCCGTCTCTGAGTATGTAA	5	121	0
TCTCCCATCTTCATCCCCCACTTCCCTCTTTTATT	5	222	1
          * ****  *  ****
MAP Score: 16.3286

Motif 3
TTTATAAGTTATAAGCAATAAAATTGAAGGAAGAAGAAAGG	0	36	0
ATAACTTATAAATTTGGGAAATATTTGGCTAGATTATTATA	0	65	1
ATTTGGCTAGATTATTATAAAACTTTAAGTAGTAATGCTAA	0	87	1
AAACTTAAAAATAAAAAGAGACATTTTTCCATAACTTTTTA	0	125	0
ACAAAGGCCCAAAGCTGGTAAAGTTTTATAAGCTGAATAGT	1	24	0
GAGGACATTAATAAACGCTGAGGTTTACATAGGACAAAGGC	1	57	0
AGCGTTTATTAATGTCCTCAACTTTTCTCAATGTGCGAAAA	1	79	1
AAATTCGAGAAATATAGAAAAAATTTTCGCACATTGAGAAA	1	102	0
AAATAATTCCAAAACTGATAAAATTTTAAGAATAATTTCGA	1	149	1
GATTCATCTAATATTCCGAAAATTTTATATAGGGTATGTTG	1	191	1
AACATCGATGAAATATAAAAACCTTATTTGAGAAGTCGAG 	2	19	1
GGTCACATAAATATTTTGAAAGGTTTTTATTTAATCCATGC	4	39	1
TGGAATCTCAATTGTTACAAACTTCTCCTCATCTCCCATCT	5	191	1
TCTTTTATTAATGGCTTTTAAGCTTTAGCTAAAATGTTAAA	5	248	1
GCTTTAGCTAAAATGTTAAAAATTCTAATAAACAGGAAGGC	5	269	1
CCAGACAAAAATTACAGTTAAGCTTTTATTACAAAATTTCC	6	23	1
ATTTCGATATATAAATAAAAACCTTTTCGTAAAGGTTTATA	7	28	1
          ***     ***  ***    *
MAP Score: 12.996

Motif 4
TTTATTAATGTCCTCAACTTTTCTCAATGTGCGAAAA	1	83	1
AAAAACCTTTTCGTAAAGGTTTATATACCCAAGCTTC	7	44	1
CATCTAATATTCCGAAAATTTTATATAGGGTATGTTG	1	195	1
TAAGTAGTAATGCTAAAAAGTTATGGAAAAATGTCTC	0	112	1
TTTCTCAATGTGCGAAAATTTTTTCTATATTTCTCGA	1	102	1
ATTCCAAAACTGATAAAATTTTAAGAATAATTTCGAT	1	154	1
GGCTAGATTATTATAAAACTTTAAGTAGTAATGCTAA	0	91	1
AAATTTCCCTTACTAAAACTTGGTGTAGTAA      	6	56	1
TTTAAGCTTTAGCTAAAATGTTAAAAATTCTAATAAA	5	264	1
AATAAGGGTCACATAAATATTTTGAAAGGTTTTTATT	4	33	1
CTTATAAATTTGGGAAATATTTGGCTAGATTATTATA	0	69	1
CGTTTTTGGAATCTCAATTGTTACAAACTTCTCCTCA	5	185	1
GGCCCAAAGCTGGTAAAGTTTTATAAGCTGAATAGTA	1	23	0
TTTTCTATATTTCTCGAATTTTGTCGAAAATAATTCC	1	122	1
AGTTTTAGTAAGGGAAATTTTGTAATAAAAGCTTAAC	6	39	0
CTCTATCTTCTCGTAAAGCGTTTTTGGAATCTCAATT	5	167	1
GAGGGAGGTCTTAGCAAGCTTGGAGGAGGAAGAGGAG	5	74	0
TCCTATGTAAACCTCAGCGTTTATTAATGTCCTCAAC	1	64	1
    GTGGTCACCTATAAGGTTATTTACCATGCCAGT	3	33	0
          * *****  ***    *
MAP Score: 12.7909

Motif 5
GGAAGAAGAAAGGAGATCTGAGAAAAGTGGGAAAAGAA	0	11	0
GCTTATAACTTATAAATTTGGGAAATATTTGGCTAGAT	0	61	1
TAGTAATGCTAAAAAGTTATGGAAAAATGTCTCTTTTT	0	116	1
ATAAGGTAGCAAATTATACATGAAAACTTAAAAATAAA	0	151	0
TATATTGGCAAGTTTATGTAGGAAATCTTAATATATTA	0	204	1
TATAAGCTGAATAGTATCTTGAAAATAAT         	1	1	0
CCTCAACTTTTCTCAATGTGCGAAAATTTTTTCTATAT	1	94	1
ATTATTTTCGACAAAATTCGAGAAATATAGAAAAAATT	1	118	0
TGAATCATCGAAATTATTCTTAAAATTTTATCAGTTTT	1	159	0
CATACCCTATATAAAATTTTCGGAATATTAGATGAATC	1	191	0
   CAGCTAAAGAACATCGATGAAATATAAAAACCTTA	2	7	1
CTTAACACCTAGAGGATTATCGAAATAAGGGTCACATA	4	10	1
ATCTTCTCGTAAAGCGTTTTTGGAATCTCAATTGTTAC	5	171	1
CTACACCAAGTTTTAGTAAGGGAAATTTTGTAATAAAA	6	46	0
          * *  **    ***** *
MAP Score: 12.0887

Motif 6
CAATAAAATTGAAGGAAGAAGAAAGGAGATCTGAG	0	27	0
TGATATATTGGCAAGTTTATGTAGGAAATCTTAAT	0	201	1
AGGGTATGTTGATGGTTGATGTGGGTGGTGCCTAT	1	221	1
AGGAAGAGGAGAAGGTTAAGGAGAGGCTTAGAGCC	5	20	0
CAAGCTTGGAGGAGGAAGAGGAGGAAGAGGTTTTC	5	62	0
GGGGGATGAAGATGGGAGATGAGGAGAAGTTTGTA	5	206	0
          *  **  ** *****
MAP Score: 0.163571