AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_operons033_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944256542
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH0520	154	333aa long hypothetical dehydrogenase
#1	PH0742	300	256aa long hypothetical protein
#2	PH1113	99	337aa long hypothetical protein
#3	PH1391	56	348aa long hypothetical protein

Motif 1
ATTATAATAACTTCTAGCCCTTCCATACTAAG	0	21	0
CTAAGGATTCTAAATATCCCTTAATTCTTTGG	0	66	0
GGGAGCTAAACCACTAGCCCTCGCTAGCT   	1	7	0
TGGTCATACCGTTAGACCCCTCTTCTTCCCTG	1	94	0
GATGATGGGGCAACGATCCCCTTTGAAGGTAA	1	147	0
AGGGATTGGCCTAGAAGCCCTCGATGATGGGG	1	169	0
ATGAGTTCTTCCATTAGCTCTCCACCCGCACC	1	243	1
TTATCTTCACTTATAATCCCCCAA        	1	286	1
GGTAGGTGGTTCATCACCCCTCAGCCGGGAGT	2	25	1
          GCTTTATCCCACTCACTTTAAA	3	44	0
          ***  *******
MAP Score: 7.75703

Motif 2
    GCCCCTCCCCTCTTAGTATGGAAGGGCTAG	0	6	1
TGGTTTAGCTCCCATCACGGCGAGATCATTTACC	1	26	1
CTACCTATGTCACCTCCAGGGAAGAAGAGGGGTC	1	78	1
GGATCGTTGCCCCATCATCGAGGGCTTCTAGGCC	1	160	1
TCTAGGCCAATCCCTCCAGCAGAGTTTAAGGTTA	1	186	1
     GCTTTCACCTCAGCCGGTAGGTGGTTCAT	2	5	1
TGGTTCATCACCCCTCAGCCGGGAGTAGTTCATC	2	31	1
          ******  ** * *
MAP Score: 7.70318

Motif 3
TCCATACTAAGAGGGGAGGGGC         	0	1	0
TCACCCCTCAGCCGGGAGTAGTTCATCATTA	2	38	1
TAAAGCTTGAGCATGGTGCGGGTGGAGAGCT	1	258	0
AAATGATCTCGCCGTGATGGGAGCTAAACCA	1	26	0
AAACTCTGCTGGAGGGATTGGCCTAGAAGCC	1	182	0
TTTCACCTCAGCCGGTAGGTGGTTCATCACC	2	12	1
CCCTCTTCTTCCCTGGAGGTGACATAGGTAG	1	78	0
AGGTAGACTAGCGGTTAGCGGAACGGTAAAT	1	53	0
ACTCCCGGCTGAGGGGTGATGAACCACCTAC	2	26	0
TCCCCTCTTAGTATGGAAGGGCTAGAAGTTA	0	15	1
ACTTTAAATACAATGGATAGGTAAATAATTT	3	21	0
CATTGTATTTAAAGTGAGTGGGATAAAGC  	3	37	1
TAATTCTTTGGTATGGAAGAGAAAATTATAA	0	46	0
ATGACGATCTAAATGGTGATGAA        	0	141	1
          ******** **
MAP Score: 7.43061

Motif 4
       GCCCCTCCCCTCTTAGTATGGAAGGGCTAGAAGTTATT	0	3	1
ATAATTTTCTCTTCCATACCAAAGAATTAAGGGATATTTAGAATC	0	48	1
GTTTAGCTCCCATCACGGCGAGATCATTTACCGTTCCGCTAACCG	1	28	1
TTAGACCCCTCTTCTTCCCTGGAGGTGACATAGGTAGACTAGCGG	1	70	0
TGAAGGTAAACACCTTGTCTTCACAATAGATGGTCATACCGTTAG	1	111	0
CTTCAAAGGGGATCGTTGCCCCATCATCGAGGGCTTCTAGGCCAA	1	151	1
CTTCTAGGCCAATCCCTCCAGCAGAGTTTAAGGTTAAATTCTTTA	1	184	1
GTAGGTGGTTCATCACCCCTCAGCCGGGAGTAGTTCATCATTAGT	2	26	1
         GCATCCACCCAAAATTATTTACCTATCCATTGTATT	3	1	1
          * **    *   *   *  * ** *
MAP Score: 6.37034

Motif 5
         GCCCCTCCCCTCTTAGTATGGAAGGGC	0	1	1
GGAGCTAAACCACTAGCCCTCGCTAGCT        	1	2	0
ACGGTAAATGATCTCGCCGTGATGGGAGCTAAACCA	1	26	0
ACGGCGAGATCATTTACCGTTCCGCTAACCGCTAGT	1	42	1
TTAGACCCCTCTTCTTCCCTGGAGGTGACATAGGTA	1	79	0
CAAAGGGGATCGTTGCCCCATCATCGAGGGCTTCTA	1	154	1
TGAGTTCTTCCATTAGCTCTCCACCCGCACCATGCT	1	244	1
GGTGATGAACCACCTACCGGCTGAGGTGAAAGC   	2	7	0
GTAGGTGGTTCATCACCCCTCAGCCGGGAGTAGTTC	2	26	1
         GCTTTATCCCACTCACTTTAAATACAA	3	39	0
          * **  *****   **
MAP Score: 0.77055