AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_operons026_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944256379
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH1107	299	299aa long hypothetical protein
#1	PH1516	149	303aa long hypothetical dihydroorotate dehydrogenase
#2	PH1517	93	460aa long hypothetical protein
#3	PH1739	113	212aa long hypothetical protein

Motif 1
AAGCTAATTGGGGGGAGTGAA          	3	102	1
TATCCTGATAGAGGGAGATAAAATA      	1	4	0
AAAGGTTCCGGGTGGATGGAAATCCTTTTAA	3	45	1
AAAGAGATCAAATGGAGAGAAGGAATGAAGG	0	185	0
ATGGAGATCTAGTGGAGGTAATTCCGGTAGT	0	61	0
GTGATTGGAAGGGGAATAGAGAAAGAGATCA	0	206	0
AGGATATTCTGAGGGAGGTCGGCTTTAATAC	0	151	0
AAGATCCTGGGAGGGATAAAA          	2	82	1
CTTAAAAATGAGGGGGTTGAGATGATAAGGG	0	242	0
GGAGAGAAGGAATGAAGGTAAAGGATATTCT	0	172	0
TTTTTAAGGAGGTGAGGATAAAAATATTCTC	0	265	1
AAAAGGAGGTCAGGGATGGAGATCTAGTGGA	0	76	0
TATGAAGGATAGGGTAGAAAAGGACTAGGGA	3	15	0
          ******* ***
MAP Score: 9.981

Motif 2
AGATCTCCATCCCTGACCTCCTTTTCTTCTAAC	0	82	1
TTTGCTATCGCACTCTCAGTATTAAAGCCGACC	0	133	1
CTCAGAATATCCTTTACCTTCATTCCTTCTCTC	0	169	1
TTACCTTCATTCCTTCTCTCCATTTGATCTCTT	0	182	1
TGATCTCTTTCTCTATTCCCCTTCCAATCACTT	0	206	1
CCCTTCCAATCACTTTCACCCTTATCATCTCAA	0	224	1
ATCATCTCAACCCCCTCATTTTTAAGGAGGTGA	0	247	1
AATATTTTTATCCTCACCTCCTTAAAAATGAGG	0	260	0
TATAACTTTTCCCGTCTCATTATGTCGATAATA	2	23	0
    TTTCTTCCCTAGTCCTTTTCTACCCTATC	3	6	1
TCCTTTTCTACCCTATCCTTCATAAAGGTTCCG	3	22	1
        TTCACTCCCCCCAATTAGCTTGACA	3	98	0
          ****  ** ****
MAP Score: 9.90164

Motif 3
GGAGGTCAGGGATGGAGATCTAGTGGAGGTAATTCCGGTAGT	0	61	0
AAAAGTAAATGGAAAAGTAGCGTTAGAAGAAAAGGAGGTCAG	0	94	0
CTTTAATACTGAGAGTGCGATAGCAAAAGTAAATGGAAAAGT	0	118	0
CAAATGGAGAGAAGGAATGAAGGTAAAGGATATTCTGAGGGA	0	166	0
GAAAGTGATTGGAAGGGGAATAGAGAAAGAGATCAAATGGAG	0	199	0
TGAGGGGGTTGAGATGATAAGGGTGAAAGTGATTGGAAGGGG	0	223	0
AACTAGGGCTGATATCCTGATAGAGGGAGATAAAATA     	1	5	0
TTATTATCGACATAATGAGACGGGAAAAGTTATAACATTTGT	2	22	1
ATCAAAAATGGAAAGATCCTGGGAGGGATAAAA         	2	70	1
CTATCCTTCATAAAGGTTCCGGGTGGATGGAAATCCTTTTAA	3	34	1
TTTAACTAGTTAAAAATATTTGGTAAATGTCAAGCTAATTGG	3	71	1
          ** *       ** *** *  *
MAP Score: 7.99295

Motif 4
          AATTTATAAATATTTTTATGGCCG	0	0	1
TATGGCCGAAAAGTTAGATAAATTAGCCTCCAGA	0	26	1
TAAGGAGGTGAGGATAAAAATATTCTCTGGTTGA	0	269	1
ATTACAGTTTAATATAAAAACCTTATTTGAAACT	1	121	1
GAGACGGGAAAAGTTATAACATTTGTCGAAAAAT	2	38	1
TATTTTTAACTAGTTAAAAGGATTTCCATCCACC	3	55	0
TCCTTTTAACTAGTTAAAAATATTTGGTAAATGT	3	67	1
          ****** **   **
MAP Score: 4.41804

Motif 5
GGTCAGGGATGGAGATCTAGTGGAGGTAATTCCGGTAGTT	0	60	0
AGTAGCGTTAGAAGAAAAGGAGGTCAGGGATGGAGATCTA	0	81	0
CAAATGGAGAGAAGGAATGAAGGTAAAGGATATTCTGAGG	0	168	0
TAGAGAAAGAGATCAAATGGAGAGAAGGAATGAAGGTAAA	0	181	0
GGTGAAAGTGATTGGAAGGGGAATAGAGAAAGAGATCAAA	0	204	0
GGGGGTTGAGATGATAAGGGTGAAAGTGATTGGAAGGGGA	0	222	0
TCACCTCCTTAAAAATGAGGGGGTTGAGATGATAAGGGTG	0	240	0
CAACCCCCTCATTTTTAAGGAGGTGAGGATAAAAATATTC	0	254	1
CAAAAATGGAAAGATCCTGGGAGGGATAAAA         	2	72	1
AACCTTTATGAAGGATAGGGTAGAAAAGGACTAGGGAAGA	3	12	0
TCCTTCATAAAGGTTCCGGGTGGATGGAAATCCTTTTAAC	3	37	1
GTAAATGTCAAGCTAATTGGGGGGAGTGAA          	3	93	1
          *       ** *** * ***
MAP Score: 3.98282

Motif 6
AGATCTCCATCCCTGACCTCCTTTTCTTCTAAC	0	82	1
TTTCCATTTACTTTTGCTATCGCACTCTCAGTA	0	121	1
CTCAGAATATCCTTTACCTTCATTCCTTCTCTC	0	169	1
TACCTTCATTCCTTCTCTCCATTTGATCTCTTT	0	183	1
TCCATTTGATCTCTTTCTCTATTCCCCTTCCAA	0	200	1
TTCTCTATTCCCCTTCCAATCACTTTCACCCTT	0	214	1
ATCACTTTCACCCTTATCATCTCAACCCCCTCA	0	232	1
AATATTTTTATCCTCACCTCCTTAAAAATGAGG	0	260	0
ATAAGATAAGGCCTCCCTTTAATAGAATTGACA	1	66	1
AATGTTATAACTTTTCCCGTCTCATTATGTCGA	2	28	0
    TTTTATCCCTCCCAGGATCTTTCCATTTT	2	74	0
CTTCCCTAGTCCTTTTCTACCCTATCCTTCATA	3	13	1
TAGTTAAAAGGATTTCCATCCACCCGGAACCTT	3	46	0
        TTCACTCCCCCCAATTAGCTTGACA	3	98	0
          ***** ** ** *
MAP Score: 3.77054

Motif 7
GTTAGAAGAAAAGGAGGTCAGGGATGGAGATCTAGTGGAG	0	75	0
AAGTGATTGGAAGGGGAATAGAGAAAGAGATCAAATGGAG	0	199	0
CTCACCTCCTTAAAAATGAGGGGGTTGAGATGATAAGGGT	0	241	0
CAAAAATGGAAAGATCCTGGGAGGGATAAAA         	2	72	1
ATCCTTCATAAAGGTTCCGGGTGGATGGAAATCCTTTTAA	3	36	1
GGTAAATGTCAAGCTAATTGGGGGGAGTGAA         	3	92	1
          ***      ** **  * **
MAP Score: 2.33416

Motif 8
ATTACCTCCACTAGATCTCCATCCCTGACCTCCTTTTCTTCTAAC	0	70	1
TCCTTTTCTTCTAACGCTACTTTTCCATTTACTTTTGCTATCGCA	0	100	1
TTTGCTATCGCACTCTCAGTATTAAAGCCGACCTCCCTCAGAATA	0	133	1
TAAAGCCGACCTCCCTCAGAATATCCTTTACCTTCATTCCTTCTC	0	155	1
CTTCTCTCCATTTGATCTCTTTCTCTATTCCCCTTCCAATCACTT	0	194	1
CTATTCCCCTTCCAATCACTTTCACCCTTATCATCTCAACCCCCT	0	218	1
TTTTATCTCCCTCTATCAGGATATCAGCCCTAGTTGGATGATAGC	1	12	1
   TTTCTTCCCTAGTCCTTTTCTACCCTATCCTTCATAAAGGTT	3	7	1
          *    **   **  *   *  * **
MAP Score: 1.4942

Motif 9
CCGGAATTACCTCCACTAGATCTCCATCCCTGACCTC	0	65	1
TTCCATTTACTTTTGCTATCGCACTCTCAGTATTAAA	0	122	1
AGTATTAAAGCCGACCTCCCTCAGAATATCCTTTACC	0	150	1
TCCTTTACCTTCATTCCTTCTCTCCATTTGATCTCTT	0	178	1
TTCTCTCCATTTGATCTCTTTCTCTATTCCCCTTCCA	0	195	1
TATTCCCCTTCCAATCACTTTCACCCTTATCATCTCA	0	219	1
CCCTTATCATCTCAACCCCCTCATTTTTAAGGAGGTG	0	242	1
   TATTTTATCTCCCTCTATCAGGATATCAGCCCTA	1	7	1
ATGTTATAACTTTTCCCGTCTCATTATGTCGATAATA	2	23	0
         TTTTATCCCTCCCAGGATCTTTCCATTT	2	75	0
CTAGTCCTTTTCTACCCTATCCTTCATAAAGGTTCCG	3	18	1
          **   **  ****  **
MAP Score: 1.12952