AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_operons006_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944255494
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH0437	263	367aa long hypothetical protein
#1	PH0438	58	339aa long hypothetical adenylosuccinate synthetase
#2	PH0439	31	255aa long hypothetical competence-damage protein
#3	PH0443	134	428aa long hypothetical methyl-accepting chemotaxis protein
#4	PH0479	31	277aa long hypothetical methyl-accepting chemotaxis protein
#5	PH0481	263	280aa long hypothetical chemotaxis protein methyltransferase
#6	PH0487	266	212aa long hypothetical protein
#7	PH0490	179	162aa long hypothetical protein
#8	PH0493	300	246aa long hypothetical protein
#9	PH1853	250	218aa long hypothetical protein
#10	PH1971	51	258aa long hypothetical protein

Motif 1
CCCTTCTAAGCTCTTCAATTGATGCTGTCT	8	181	0
    AATCCACCCCTCAACTTGGATTTTGT	5	247	0
GGTTTACCAGCTCCTCAAGTTGATAGATTT	6	59	1
GACTTATGAACTCTTCATTTTGCTCACTAC	5	18	1
TGCAATAATTCCCCTCATCTTCTCAACTAT	8	231	0
TTAAATATTCCTCTTCTAATTATACCTTTG	10	31	1
CGATTGGAGTCTCCTTAATTCTCTTCTCAA	0	69	0
AAGTTTTCGTCTCTTCTTTTAATGAAGCCT	5	78	1
TCTTCTCAAACTCTTCACCTAATATTTTGA	0	48	0
ATGCTGTCTGCTCTTCAACAGCAGAGCTTA	8	160	0
GTAGAGATTTCTCTTCTTATCGACATA   	0	7	0
          CTCCTTTATTTCCTTATCGA	4	21	0
 TCAAGCTATCTCTTTAAATATTGTGTATG	9	9	1
TACCAGGGATCTCCTCAAAATATTAGGTGA	0	34	1
TAATTATGCTCCCTTCTTTTTATAACCGTT	3	61	0
TTTTAAGGTACCCCTTTACTTACCCTTTGG	1	30	1
TCTCACTGGTCTCCTGAAGTAGGGTTGCGA	8	13	0
         ACTCCTTACCAAAGGGTAAGT	1	47	0
CTCCTTAATTCTCTTCTCAAACTCTTCACC	0	59	0
TCACATAATACTCCTCATACTTTTCGATTG	0	93	0
CTTTCCAAGGCTCTTGATCACTATATCTCT	6	155	0
GGCGCTTCCACTCCGCTTCTCTAGCCTTCA	0	120	0
CCCTGCAAAGCCCCTGACATTTGATAGGAA	6	185	0
          **********
MAP Score: 17.7039

Motif 2
TCAAAATATTAGGTGAAGAGTTTGAGAAGAGAAT	0	48	1
TGAAGGCTAGAGAAGCGGAGTGGAAGCGCCTAAG	0	120	1
AACGGTTATAAAAAGAAGGGAGCATAATTATTGA	3	61	1
GTAGTGAGCAAAATGAAGAGTTCATAAGTCTTCC	5	14	0
AGGCTTCATTAAAAGAAGAGACGAAAACTTTTTT	5	74	0
TAAACTTCAAAAATGGAGATGTAAAACTACTAGG	5	105	0
ATTGTATAGAAGCCGAAAATATCATGATCGTCTT	5	204	1
ACAAAATCCAAGTTGAGGGGTGGATT        	5	247	1
    AGTTCTAAGGGGAGAGATAATTCCCGTAAT	6	6	1
GGAGCTGGTAAACCAAAGAGCTCATGCAACATTA	6	39	0
CTCGTGAAAAAGCTGGAAAGCCAAGTTAGCGGAG	7	143	1
AAGCCAAGTTAGCGGAGAGGTTGAAACCA     	7	160	1
TCTGCTCTTCAACAGCAGAGCTTACCTCCTCAGC	8	150	0
AGACAGCATCAATTGAAGAGCTTAGAAGGGCCGC	8	181	1
TTAGAGATATAGTTGAGAAGATGAGGGGAATTAT	8	223	1
CTAAAAATTTAGGAAGGGAGGTCAGACCTTAAAC	8	263	0
AAGACTTTCAAGCTGGAGGGACAATAGTTCGGAG	9	60	0
          **  ****** * *
MAP Score: 12.7276

Motif 3
AGGCTAGAGAAGCGGAGTGGAAGCGCCTAA	0	123	1
CTTTTAATGAAGCCTAGTAGTTTTACATCT	5	93	1
CCATTTTTGAAGTTTAGAAAATCTACAAAG	5	123	1
TTGTGTAGGTAGCTTTGTAGATTTTCTAAA	5	135	0
TTATGCACGTAGTTGTGTAGGTAGCTTTGT	5	147	0
ACAAAATCCAAGTTGAGGGGTGGATT    	5	247	1
  TGAGAAAGAGCTTGGAAGGTCTGACCTG	7	8	1
AAATGTTAATAGTGTTGTGGTTTTCAAGTC	7	40	1
CTTTTTCACGAGTTTTGTGAATGATTCAGG	7	125	0
AAGCCAAGTTAGCGGAGAGGTTGAAACCA 	7	160	1
TTTAGCGGCAAGCGCTGAAGAAACCACGGC	8	116	1
AACCACGGCTAGCGCTGAGGAGGTAAGCTC	8	137	1
TCAATTGAAGAGCTTAGAAGGGCCGCACAG	8	189	1
GCCGCACAGGAGCTTAGAGATATAGTTGAG	8	210	1
TTAGAGATATAGTTGAGAAGATGAGGGGAA	8	223	1
          **********
MAP Score: 11.2608

Motif 4
AAGGCTAGAGAAGCGGAGTGGAAGCGCCTAAGAA	0	122	1
AACAAAATCCAAGTTGAGGGGTGGATT       	5	246	1
    AGTTCTAAGGGGAGAGATAATTCCCGTAAT	6	6	1
TAGTCGATCATGGGGCCCAGAAGGTTGCAATAGG	6	99	1
TATAGTGATCAAGAGCCTTGGAAAGTTCCTATCA	6	160	1
ATCAAATGTCAGGGGCTTTGCAGGGGCTACAATA	6	190	1
     TGAGAAAGAGCTTGGAAGGTCTGACCTGA	7	5	1
AAGTTCTATAAAGAGGATATTAGGGTCGAAAGTT	7	71	1
AAACCACGGCTAGCGCTGAGGAGGTAAGCTCTGC	8	136	1
GCATCAATTGAAGAGCTTAGAAGGGCCGCACAGG	8	186	1
CTAAATTTTTAGGGGGTGAGAAAGT         	8	285	1
GGAGGGACAATAGTTCGGAGTAAGAACTTAGTGC	9	46	0
ATACGTTATAAAGTTTGGCGGAGGTGGA      	9	232	1
          *** ** * * ***
MAP Score: 9.59803

Motif 5
GTATTATGTGAAGGCTAGAGAAGCGGAGTGGAA	0	112	1
GCGGAGTGGAAGCGCCTAAGAAGCTTTACGACA	0	134	1
CTCCTTACCAAAGGGTAAGTAAAGGGGTACCTT	1	34	0
GAGCAAAATGAAGAGTTCATAAGTCTTCCTGGG	5	10	0
TATCAACTTGAGGAGCTGGTAAACCAAAGAGCT	6	51	0
TAGTCGATCATGGGGCCCAGAAGGTTGCAATAG	6	99	1
AGGTTGCAATAGGGGTTGATGAGCTGTTACATA	6	120	1
TATAGTGATCAAGAGCCTTGGAAAGTTCCTATC	6	160	1
ATCAAATGTCAGGGGCTTTGCAGGGGCTACAAT	6	190	1
TAGACATTGGAGGGCTGCTTGGAG         	6	252	1
     TGAGAAAGAGCTTGGAAGGTCTGACCTG	7	5	1
TCAAATCGTTAAGACCCAGGAGGAGGTTGATAA	8	62	1
TAAATCCCTTAGGGCCCTCGAGAATTTAGCGGC	8	92	1
TTTAGCGGCAAGCGCTGAAGAAACCACGGCTAG	8	116	1
AACCACGGCTAGCGCTGAGGAGGTAAGCTCTGC	8	137	1
GCATCAATTGAAGAGCTTAGAAGGGCCGCACAG	8	186	1
AGGGCCGCACAGGAGCTTAGAGATATAGTTGAG	8	207	1
CTAAATTTTTAGGGGGTGAGAAAGT        	8	285	1
          ******   ****
MAP Score: 9.36572

Motif 6
ATATTAGGTGAAGAGTTTGAGAAGAGAATT	0	53	1
ATAAAAAGAAGGGAGCATAATTATTGAATA	3	68	1
AATCCAAGTTGAGGGGTGGATT        	5	251	1
    AGTTCTAAGGGGAGAGATAATTCCCG	6	6	1
TATCAACTTGAGGAGCTGGTAAACCAAAGA	6	54	0
ATCAAATGTCAGGGGCTTTGCAGGGGCTAC	6	190	1
     TGAGAAAGAGCTTGGAAGGTCTGAC	7	5	1
AAGTTCTATAAAGAGGATATTAGGGTCGAA	7	71	1
CAAGTTAGCGGAGAGGTTGAAACCA     	7	164	1
GAGAGAATGTCGGAGGTTAAGGATCAAATC	8	39	1
AAGACCCAGGAGGAGGTTGATAAATCCCTT	8	72	1
GCTAGCGCTGAGGAGGTAAGCTCTGCTGTT	8	144	1
GCATCAATTGAAGAGCTTAGAAGGGCCGCA	8	186	1
AGGGCCGCACAGGAGCTTAGAGATATAGTT	8	207	1
CTAAATTTTTAGGGGGTGAGAAAGT     	8	285	1
TAAAGTTTGGCGGAGGTGGA          	9	240	1
          **********
MAP Score: 5.49314

Motif 7
GGTGAAGAGTTTGAGAAGAGAATTAAGGAGACT	0	59	1
ATGTGAAGGCTAGAGAAGCGGAGTGGAAGCGCC	0	117	1
AAAATCCAAGTTGAGGGGTGGATT         	5	249	1
GCAACCCTACTTCAGGAGACCAGTGAGAGAATG	8	15	1
ACGGCTAGCGCTGAGGAGGTAAGCTCTGCTGTT	8	141	1
AGCTCTGCTGTTGAAGAGCAGACAGCATCAATT	8	162	1
ACAGCATCAATTGAAGAGCTTAGAAGGGCCGCA	8	183	1
AGAGATATAGTTGAGAAGATGAGGGGAATTATT	8	225	1
TTCCTAAATTTTTAGGGGGTGAGAAAGT     	8	282	1
          ********   **
MAP Score: 3.82588

Motif 8
TCTTTTAATGAAGCCTAGTAGTTTTACATCT	5	92	1
GTTGTGTAGGTAGCTTTGTAGATTTTCTAAA	5	135	0
ATGAGCTCTTTGGTTTACCAGCTCCTCAAGT	6	48	1
GTCGATCATGGGGCCCAGAAGGTTGCAATAG	6	101	1
CAAATGTCAGGGGCTTTGCAGGGGCTACAAT	6	192	1
   TGAGAAAGAGCTTGGAAGGTCTGACCTG	7	7	1
AATAGTGTTGTGGTTTTCAAGTCGAAGTTCT	7	47	1
TCCGCTAACTTGGCTTTCCAGCTTTTTCACG	7	145	0
AAATCCCTTAGGGCCCTCGAGAATTTAGCGG	8	93	1
ATTTAGCGGCAAGCGCTGAAGAAACCACGGC	8	115	1
CTGAGGAGGTAAGCTCTGCTGTTGAAGAGCA	8	151	1
ATCAATTGAAGAGCTTAGAAGGGCCGCACAG	8	188	1
TCCGAACTATTGTCCCTCCAGCTTGAAAGTC	9	61	1
          ******** **
MAP Score: 2.76124