AlignACE 3.0 10/20/99
AlignACE2 -i PA/PA_operons025_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944250175
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PAB2109	60	PAB2109
#1	PAB0315	300	hypothetical protein
#2	mpg	70	PAB0317
#3	srp54	38	PAB0320
#4	PAB2025	300	PAB2025
#5	PAB0350	185	PAB0350
#6	PAB1983	138	PAB1983
#7	hypA	70	PAB0399
#8	PAB0463	111	hypothetical protein
#9	PAB1262	300	hypothetical protein

Motif 1
     AATTCAACCTCGGAAATGATTTATAT	0	5	1
GTTGATGAGAAACCCTTGAGGTTATAAATCT	1	267	0
TTCTGAATTTAACCTTGGAAAGGTGAAGCAC	3	16	1
AAGTGTTCAAAATCTTGGAAATCAAATGCAC	5	55	0
AAGATTTTGAACACTTTGAAGTCTTTTAGCT	5	70	1
TTCGGAGTAGAGACTTTGAGGTGAACGAATT	6	45	1
        TAACACGTGGAGGTATTGCTTGT	8	2	1
GAACTTATTCACTCTTGGATACTTCGTATCT	8	36	1
CTCGTAAATCAACCTTGGAAGATACGAAGTA	8	55	0
CATCCTTCGAAATCCTTGAAATTATGTTTAA	9	165	1
ATTCGGGAATACCCCTTGAGAACGTGCT   	9	282	1
          ** ********
MAP Score: 9.51245

Motif 2
ATGATTTATATAAGAATTCCTAGTTTCAGATAAG	0	25	1
GGCTCCTTTATTCAAAGTCCTAGATGTTCAATAC	1	70	1
GGATAAGTGAGTATAATTCCTTGACTCAGGCCGT	1	153	1
GGCCGTTGCTTTTTAGGCCCTTTACTCTTATTTT	1	181	1
GATATTTGAATTCAAATTCCTCTTGATACAAAAA	1	233	1
ACCCTTGAGGTTATAAATCTTTTTTGTATCAAGA	1	253	0
GTCGTGTTGATGAGAAACCCTTGAGGTTATAAAT	1	269	0
CTTCAAAGTGTTCAAAATCTTGGAAATCAAATGC	5	57	0
TTTTGAACACTTTGAAGTCTTTTAGCTTTAATAA	5	74	1
ACCTTTTCATTTTTAAACCCTAGTGCACAACTAT	7	32	1
TGAGTCATCCTTCGAAATCCTTGAAATTATGTTT	9	160	1
          **  ** **** **
MAP Score: 8.33454

Motif 3
   AATTCAACCTCGGAAATGATTTATATAAGAATTC	0	7	1
ACTCTTATTTTCCCTAAAATGATGTCTACGATATTTG	1	204	1
TGATGAGAAACCCTTGAGGTTATAAATCTTTTTTGTA	1	259	0
TCTTTTATAACCATAACATTTAATATTCCCGCCCTTG	2	22	1
AACCCAGTTTCCGTAGAACTAAATAGTGTGGAAAGCC	4	17	1
CGTAGTGTTTCCGTAGAACTAAATAGTATAGATTGCT	4	83	1
GGCAGAGTTCCCATAGAAGTTAACATAGCAACAGATT	4	163	1
AATATATGATCCCTAAAATTTAAACCTTGTGCATTTG	5	27	1
GTGTTCAAAATCTTGGAAATCAAATGCACAAGGTTTA	5	47	0
CTTCCATTCTTCATTGAAATTATGTCTGAGTCATCCT	9	134	1
TCCTTCGAAATCCTTGAAATTATGTTTAAGAGAGGAA	9	167	1
          ** * *** * **   *
MAP Score: 6.46517

Motif 4
GAATTCCTAGTTTCAGATAAGTGGTGTAATG	0	38	1
TGGCTGGAATTTTAGGTTTGGCAACGGTTCT	1	120	1
GTCAACCAAATTTCGGCGAGGAGG       	5	171	1
TAGAAATAGTTTTCGGAGTAGAGACTTTGAG	6	34	1
ACTGCAATTTTGTAGGGGTGGTACATC    	6	121	1
TCGATCACCATTTAAATGTAGACCTTTTCAT	7	11	1
AGCTAATTACTTTAGGAGAGACTGTATCAAT	9	45	1
ATCATATTCGTTTAGAAGTGGAAGTTTTATT	9	73	0
TCAGACATAATTTCAATGAAGAATGGAAGAT	9	132	0
TGAAATTATGTTTAAGAGAGGAAATAGGGAA	9	181	1
          ****** ****
MAP Score: 5.58344

Motif 5
TTATATAAATCATTTCCGAGGTTGAATT       	0	3	0
ATTTATATAAGAATTCCTAGTTTCAGATAAGTGGT	0	28	1
 GGTGCTTCACCTTTCCAAGGTTAAATTCAGAAAA	3	14	0
ACTCAACCCAGTTTCCGTAGAACTAAATAGTGTGG	4	13	1
TATTCGTAGTGTTTCCGTAGAACTAAATAGTATAG	4	79	1
CTTGATGTTAGGTTCGGAAGGAGAACCAGCGAAAT	4	118	1
        GCTGATCCCCAGCTGTAGTTCTTTTAG	4	283	0
TTGTGCATTTGATTTCCAAGATTTTGAACACTTTG	5	53	1
GCTAGAAATAGTTTTCGGAGTAGAGACTTTGAGGT	6	32	1
TTCCAAGGTTGATTTACGAGCATTATAAATCGAAG	8	66	1
TAATTTCAAGGATTTCGAAGGATGACTCAGACATA	9	154	0
          * ***** ** *  *
MAP Score: 4.27762

Motif 6
  AATTCAACCTCGGAAATGATTTATATAAGAAT	0	8	1
TTCCTAGTTTCAGATAAGTGGTGTAATGA     	0	41	1
CTCTTATTTTCCCTAAAATGATGTCTACGATATT	1	205	1
AACCCTTGAGGTTATAAATCTTTTTTGTATCAAG	1	254	0
TATTCCCGCCCTTGTAAATTATTTGGGATTCGAC	2	45	1
AGTTTCCGTAGAACTAAATAGTGTGGAAAGCCGG	4	22	1
ATTTTGAACACTTTGAAGTCTTTTAGCTTTAATA	5	73	1
TGTTTAACCTGCTAGAAATAGTTTTCGGAGTAGA	6	22	1
AAAAGGTCTACATTTAAATGGTGATCGAA     	7	5	0
TTCCATTCTTCATTGAAATTATGTCTGAGTCATC	9	135	1
CCTTCGAAATCCTTGAAATTATGTTTAAGAGAGG	9	168	1
          *   ***** ****
MAP Score: 2.83767

Motif 7
CCCAGTTTCCGTAGAACTAAATAGTGTGGAAA	4	19	1
TAGTGTTTCCGTAGAACTAAATAGTATAGATT	4	85	1
GGCTCCATTAGGTCAACCAAATTTCGGCGAGG	5	160	1
GAGACTTTGAGGTGAACGAATTTTGTAGAAAG	6	54	1
TATTGCTTGTATTGAACTTATTCACTCTTGGA	8	23	1
CTACATGCCAGTCCAACATAATCATATTCGTT	9	92	0
TTCCCGAATTAGTGAACCAAATAAATCTCAGA	9	259	0
          ** **** ****
MAP Score: 2.76858

Motif 8
GGAAATGATTTATATAAGAATTCCTAGTTTCAGATAA	0	21	1
GGGATCATGCTCTAAGGGGTTTCCTCTTGGCGTCGTT	1	18	1
GTTGGTAGAGTTTATTTGGGCTCCTTTATTCAAAGTC	1	52	1
TTTGGGCTCCTTTATTCAAAGTCCTAGATGTTCAATA	1	66	1
CTACGATATTTGAATTCAAATTCCTCTTGATACAAAA	1	229	1
TTAAACCTTGTGCATTTGATTTCCAAGATTTTGAACA	5	46	1
GTCTTTTAGCTTTAATAAGCCTCCTCTTATTTCCCAA	5	90	1
AGAGACTGTATCAATAAAACTTCCACTTCTAAACGAA	9	61	1
          *  **  **  **** *
MAP Score: 1.97777

Motif 9
GGCGTCGTTGGTAGAGTTTATTTGGGCTCC	1	46	1
CCCAGTTTCCGTAGAACTAAATAGTGTGGA	4	19	1
TAGTGTTTCCGTAGAACTAAATAGTATAGA	4	85	1
AAGTTTTTGAGTAGTGCTAAAAGAACTACA	4	267	1
CCGAAATTTGGTTGACCTAATGGAGCCTTA	5	157	0
CCATTTAAATGTAGACCTTTTCATTTTTAA	7	18	1
          **********
MAP Score: 0.767481

Motif 10
TGATGTCTACGATATTTGAATTCAAATTCCTCTTG	1	223	1
ATACAAAAAAGATTTATAACCTCAAGGGTTTCTCA	1	258	1
       GCAGTTTTCTGAATTTAACCTTGGAAAG	3	3	1
ACTCAACCCAGTTTCCGTAGAACTAAATAGTGTGG	4	13	1
TATTCGTAGTGTTTCCGTAGAACTAAATAGTATAG	4	79	1
CCCAGCTGTAGTTCTTTTAGCACTACTCAAAAACT	4	268	0
GCTAATATATGATCCCTAAAATTTAAACCTTGTGC	5	24	1
TATTTCCCAAGTTGTCTTACTTCCAACTGCATAAC	5	117	1
CCTTTTTAAGGCTCCATTAGGTCAACCAAATTTCG	5	151	1
TTTGTAGAAAGATATTTAACTTTGAGTATGAAATT	6	75	1
TAATTTCAAGGATTTCGAAGGATGACTCAGACATA	9	154	0
GCAAATGAAGGTGGTCTGAGATTTATTTGGTTCAC	9	245	1
          * * *** ** ** *
MAP Score: 0.218645

Motif 11
GACGCCAAGAGGAAACCCCTTAGAGCATGATC	1	20	0
TAAATAGTGTGGAAAGCCGGCGGCGTGGTAAT	4	36	1
TTAGTTCTACGGAAACACTACGAATATGTCGC	4	73	0
AGGTTCGGAAGGAGAACCAGCGAAATCGATGA	4	127	1
AAATTTGCCTAGAAAGACTGCAATTTTGTAGG	6	105	1
     AATTAAGAGAAACCTCGTGAGATATAT	9	5	1
AATTACTTTAGGAGAGACTGTATCAATAAAAC	9	49	1
          ***** ** ***
MAP Score: 0.157638