AlignACE 3.0 10/20/99
AlignACE2 -i PA/PA_operons025_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944250202
 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	PAB0462	219	PAB0462
#9	PAB0463	111	hypothetical protein
#10	PAB1262	300	hypothetical protein

Motif 1
GAATTCTTATATAAATCATTTCCGAGGTTGAATT     	0	5	0
AGTTAAAAGGGATCATGCTCTAAGGGGTTTCCTCTTGGC	1	10	1
TGGCGTCGTTGGTAGAGTTTATTTGGGCTCCTTTATTCA	1	45	1
TTCAATACTGGTGGCACTTTATGGTGGCTGGAATTTTAG	1	96	1
       GGTGCTTCACCTTTCCAAGGTTAAATTCAGAA	3	16	0
AGTTAACATAGCAACAGATTACTAAGGGTATTCTCCCAA	4	180	1
TAAACCTTGTGCATTTGATTTCCAAGATTTTGAACACTT	5	47	1
ACTTCCAACTGCATAACCTTTTTAAGGCTCCATTAGGTC	5	135	1
AAAATGAAAAGGTCTACATTTAAATGGTGATCGAA    	7	6	0
TAAAGGTTGGGAATAACCTTTATAGGGCTTGGCGATGAT	8	13	1
GAAATAGGGAATTATTCTTTATCCCGGTTATTTATTCAA	10	201	1
AATGAAGGTGGTCTGAGATTTATTTGGTTCACTAATTCG	10	248	1
          *    ** ***    ****
MAP Score: 8.06874

Motif 2
TATATAAATCATTTCCGAGGTTGAATT   	0	7	0
CAGGCCGTTGCTTTTTAGGCCCTTTACTCT	1	179	1
TCGTAGACATCATTTTAGGGAAAATAAGAG	1	205	0
ATCCCAAATAATTTACAAGGGCGGGAATAT	2	44	0
GGTGCTTCACCTTTCCAAGGTTAAATTCAG	3	18	0
ATAGCAACAGATTACTAAGGGTATTCTCCC	4	187	1
TACTCAAAAACTTTCCTGGGCGTTAGAGAT	4	250	0
ACAAGGTTTAAATTTTAGGGATCATATATT	5	27	0
ACTGCATAACCTTTTTAAGGCTCCATTAGG	5	142	1
AAATTGCAGTCTTTCTAGGCAAATTTCATA	6	101	0
AAAGACTGCAATTTTGTAGGGGTGGTACAT	6	117	1
TGGGAATAACCTTTATAGGGCTTGGCGATG	8	20	1
AATTTCAAGGATTTCGAAGGATGACTCAGA	10	158	0
TCTTAAACATAATTTCAAGGATTTCGAAGG	10	168	0
          **********
MAP Score: 6.80061

Motif 3
GCAGAGTTCCCATAGAAGTTAACATAGCAACA	4	164	1
GATGAGAAACCCTTGAGGTTATAAATCTTTTT	1	263	0
GGAGTAGAGACTTTGAGGTGAACGAATTTTGT	6	48	1
CCTTCGAAATCCTTGAAATTATGTTTAAGAGA	10	168	1
TTCCATTCTTCATTGAAATTATGTCTGAGTCA	10	135	1
ATTTTGAACACTTTGAAGTCTTTTAGCTTTAA	5	73	1
GTAGTGTTTCCGTAGAACTAAATAGTATAGAT	4	84	1
ACCCAGTTTCCGTAGAACTAAATAGTGTGGAA	4	18	1
TGTTCAAAATCTTGGAAATCAAATGCACAAGG	5	51	0
GATGGGCGAACTGAGAAGTGATGATGGTAGGT	8	56	1
     TAACACGTGGAGGTATTGCTTGTATTG	9	5	1
ATTCAAATATCGTAGACATCATTTTAGGGAAA	1	212	0
          * ******* **
MAP Score: 6.59736

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
GACTGACCGATTTAGACTTAGATTAGGCTAA	8	156	1
AGCTAATTACTTTAGGAGAGACTGTATCAAT	10	45	1
ATCATATTCGTTTAGAAGTGGAAGTTTTATT	10	73	0
TCAGACATAATTTCAATGAAGAATGGAAGAT	10	132	0
TGAAATTATGTTTAAGAGAGGAAATAGGGAA	10	181	1
          ****** ****
MAP Score: 5.78677

Motif 5
ACGACGCCAAGAGGAAACCCCTTAGAGCAT	1	24	0
TCGTGTTGATGAGAAACCCTTGAGGTTATA	1	272	0
GGTTCGGAAGGAGAACCAGCGAAATCGATG	4	128	1
CCTGAATTGGGAGAATACCCTTAGTAATCT	4	195	0
AACTACAGCTGGGGATCAGC          	4	290	1
         CGAGAATCACCATAGCTAATA	5	1	1
GTTAAAGGTTGGGAATAACCTTTATAGGGC	8	11	1
    AATTAAGAGAAACCTCGTGAGATATA	10	6	1
TCACTAATTCGGGAATACCCCTTGAGAACG	10	276	1
          **********
MAP Score: 5.78484

Motif 6
TGCTCTAAGGGGTTTCCTCTTGGCGTCGTTG	1	25	1
ATTTGAATTCAAATTCCTCTTGATACAAAAA	1	236	1
ATAACCTCAAGGGTTTCTCATCAACACGACG	1	273	1
TGGGAACTCTGCCTTCCTCATCGATTTCGCT	4	145	0
TTGTAGTGTAGAATACCTCTTTAGCGCCTGA	4	220	0
AGCTTTAATAAGCCTCCTCTTATTTCCCAAG	5	97	1
AGCCTAGGCTGAACTCCTCATCCCGATCCGG	8	103	0
ATATCTCACGAGGTTTCTCTTAATT      	10	4	0
GTATCAATAAAACTTCCACTTCTAAACGAAT	10	68	1
ACTAATTCGGGAATACCCCTTGAGAACGTGC	10	278	1
          ** ********
MAP Score: 5.40824

Motif 7
GTTTCCTCTTGGCGTCGTTGGTAGAGTTTATTTGGGC	1	36	1
CAGCGAAATCGATGAGGAAGGCAGAGTTCCCATAGAA	4	144	1
TACCTCTTTAGCGCCTGAATTGGGAGAATACCCTTAG	4	201	0
TTTCCTGGGCGTTAGAGATTGTAGTGTAGAATACCTC	4	232	0
TAACCTGCTAGAAATAGTTTTCGGAGTAGAGACTTTG	6	26	1
CCTTTATAGGGCTTGGCGATGATGAGTGATGGGCGAA	8	29	1
GAGCCAATCCGGATCGGGATGAGGAGTTCAGCCTAGG	8	95	1
TGATTATGTTGGACTGGCATGTAGAGTGTACTATCTT	10	100	1
TAATTTCAAGGATTTCGAAGGATGACTCAGACATAAT	10	152	0
TTCAATTCAGGCAAATGAAGGTGGTCTGAGATTTATT	10	235	1
          *     * *** *****
MAP Score: 3.78847

Motif 8
  GGTGCTTCACCTTTCCAAGGTTAAATTCAGAAAACTGC	3	10	0
CAACTGCATAACCTTTTTAAGGCTCCATTAGGTCAACCAA	5	140	1
  GATGTACCACCCCTACAAAATTGCAGTCTTTCTAGGCA	6	110	0
TTAAATGTAGACCTTTTCATTTTTAAACCCTAGTGCACAA	7	22	1
    CTGACCACCGAGTCATAGTTGTGCACTAGGGTTTAA	7	44	0
GTTGGGAATAACCTTTATAGGGCTTGGCGATGATGAGTGA	8	18	1
TGACGGACTGACCGATTTAGACTTAGATTAGGCTAACGAA	8	151	1
AGCTTAATAAACCGCTTTTCTTTTCCAGTCACG       	8	196	1
CTTGTATTGAACTTATTCACTCTTGGATACTTCGTATCTT	9	28	1
          ***  * **   **  *  *
MAP Score: 1.27977