AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_operons009_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944255670
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH1070	300	320aa long hypothetical protein
#1	PH1071	65	450aa long hypothetical protein
#2	PH1399	276	257aa long hypothetical peptidyl-prolyl cis-trans isomerase
#3	PH1400	23	298aa long hypothetical protein
#4	PH1402	81	207aa long hypothetical proteasome beta subunit precursor
#5	PH1404	68	651aa long hypothetical protein
#6	PH1481	157	120aa long hypothetical protein
#7	PH1552	27	236aa long hypothetical protein
#8	PH1553	156	260aa long hypothetical proteasome, alpha subunit
#9	PH1644	112	334aa long hypothetical centromere/microtubule binding protein

Motif 1
AATTTAATAACAAAACTTTAACATAAGGAA	0	121	1
      AATCGAAAACTTTATATACTCCAT	4	4	1
TTAAAAATTTCAAAAATTTTCGTAACAATT	0	95	1
AGTAATTATTCAAAAATTTTTCGGTGCAAG	0	255	0
AATTCTTGTTGAAAAATTTATAAGTTAAGA	9	54	0
TAACTTTTTACAAAAATTAAATAAAAACTC	0	25	1
AAACCTTTTCCAAAAATATATCCTCCTCAA	0	57	1
TAAAAACTCTCAAACCTTTTCCAAAAATAT	0	46	1
AATTTTTCAACAAGAATTTATAAAACTAGA	9	66	1
CTTTTTAAATCAAAACTCAAACAACAATTC	1	26	1
TCTGTTCTGGGAAAACTAAACCATCGGG  	4	63	1
TTAAGTAAGTCAAGACTCTTATATACCTTC	8	121	0
AACTTCTCAAGAAAGCTTAAAAGTTAACTC	2	231	1
TGAGATCATGGAAACATTTTAATATCAATG	8	53	0
GCCAAAAATCCAAAAATAATCCCAAATATC	0	226	1
CTCTGAATCTGAAAGCTCTTTGTAACCCTC	5	17	0
CTATGAAGGCCAAGGATATAGTTCTCAAAA	2	197	0
CTTCCTGGGAGAAAAGTTAATAGATTAGCC	6	124	1
GAGTAGCTTGGAAGCCTATTCTGTAATAAT	2	89	1
TACGAATACCGAAAGGTATATAAACCTTTT	6	53	1
          **********
MAP Score: 14.4058

Motif 2
AATAAAATATTGAGGAGGATATATTTTTGG	0	66	0
GATTTAAAAAGATGTGGGAGAAAAGTT   	1	7	0
AAGAGAAAAGGGAGAGGGGGGAAGAGATCA	2	23	0
TCAAAGCTTGGAAGAAGTTGTTTCCTATTA	2	115	0
CGAGAAAATTGAAGGGGTTGAAGTTAAAGG	2	163	0
TCTCAAGCAGTGAGAGGGAG          	5	58	1
TTAGACCGCCGGCGGGGGTGTGTAG     	6	5	0
GTAGTTATATTGAGGGGGTTCTTAGACCGC	6	26	0
TTTTCCTTTTTGTGGGGGTGAAACC     	7	12	1
ACTTACTTAAGGTGGAGGTGAGAAG     	8	141	1
TGTAGTGTGAGAAGGGGGTTATAGGAG   	9	7	0
GATTTTCTCTGGTGAGGTGGT         	9	101	1
          **********
MAP Score: 13.3745

Motif 3
AATTAAATAAAAACTCTCAAACCTTTTCCA	0	39	1
CAAAAATATATCCTCCTCAATATTTTATTT	0	67	1
GTCAAACTCTAATCCCTCTAAAACCTCTAT	0	173	1
          AACTTTTCTCCCACATCTTT	1	0	1
CTGATCTCTTCCCCCCTCTCCCTTTTCTCT	2	22	1
TTTTCTCTTCAACCTTTCTCCATATCTCTA	2	44	1
TTTAACTTCAACCCCTTCAATTTTCTCGCT	2	165	1
TCATAGCCTTAACTTCTCAAGAAAGCTTAA	2	221	1
CTTAAAAGTTAACTCCCCAAACGCCGATGG	2	246	1
AACAGAAGAAAAATTCTCAAGGGGAAGTGG	4	39	0
GAGCTTGAAGCAACTCTCAAGCAGTGAGAG	5	44	1
         CTCCCTCTCACTGCTTGAGAG	5	57	0
CGGTCTAAGAACCCCCTCAATATAACTACG	6	27	1
CTAATCTATTAACTTTTCTCCCAGGAAGTC	6	122	0
    GGTTTCACCCCCACAAAAAGGAAAAA	7	11	0
TCCTATAACCCCCTTCTCACACTACATTAA	9	11	1
          ACCACCTCACCAGAGAAAAT	9	102	0
          **********
MAP Score: 13.1468

Motif 4
TCCAAAAATATATCCTCCTCAATATTTTAT	0	65	1
      AACTTTTCTCCCACATCTTTTTAA	1	4	1
CAACAATTCAGTTCTTCCCCGTGCCCAA  	1	47	1
AATACTCTGATCTCTTCCCCCCTCTCCCTT	2	16	1
CTCTCCCTTTTCTCTTCAACCTTTCTCCAT	2	37	1
AGGCTTCCAAGCTACTCACCTGGGAAGGGC	2	76	0
CAGGGGCCTTTAACTTCAACCCCTTCAATT	2	157	1
AGCTTAAAAGTTAACTCCCCAAACGCCGAT	2	244	1
     GGTTCGCTCCCCATCGGCGTTTGGG	2	261	0
ATATACTCCATTTCCTCCACTTCCCCTTGA	4	23	1
GGCGGTCTAAGAACCCCCTCAATATAACTA	6	25	1
      GGTTTCACCCCCACAAAAAGGAAA	7	13	0
      CTTCTCACCTCCACCTTAAGTAAG	8	142	0
         ACCACCTCACCAGAGAAAATC	9	101	0
          **********
MAP Score: 12.3146

Motif 5
AATTAAATAAAAACTCTCAAACCTTTTCCAAAAAT	0	39	1
TAACTAAGTCAAACTCTAATCCCTCTAAAACCTCT	0	166	1
ATCCAAAAATAATCCCAAATATCTTGCACCGAAAA	0	233	1
      AACTTTTCTCCCACATCTTTTTAAATCAA	1	4	1
   CCCAGGAATACTCTGATCTCTTCCCCCCTCTC	2	7	1
TCTGATCTCTTCCCCCCTCTCCCTTTTCTCTTCAA	2	21	1
CCCTCTCCCTTTTCTCTTCAACCTTTCTCCATATC	2	35	1
CAGGGGCCTTTAACTTCAACCCCTTCAATTTTCTC	2	157	1
TCAAGCTCTGAATCTGAAAGCTCTTTGTAACCCTC	5	17	0
TGCTTGAGAGTTGCTTCAAGCTCTGAATCTGAAAG	5	32	0
GTTAATAGATTAGCCTCTAACTCTTGGT       	6	139	1
GTAAGTCAAGACTCTTATATACCTTCCGCGAGAGC	8	112	0
        CTTCTCACCTCCACCTTAAGTAAGTCA	8	139	0
          *  ***  * *****
MAP Score: 10.5071

Motif 6
GAAAAGTACTAACTTTTTACAAAAATTAAATAAAAACTC	0	16	1
AAACTCTCAAACCTTTTCCAAAAATATATCCTCCTCAAT	0	49	1
ATCCTCCTCAATATTTTATTTAAAAATTTCAAAAATTTT	0	76	1
AAAATTTCAAAAATTTTCGTAACAATTTAATAACAAAAC	0	98	1
TTTAATAACAAAACTTTAACATAAGGAAAATACTAATTT	0	123	1
TTGCACCGAAAAATTTTTGAATAATTACTATCAAAAGCT	0	256	1
ACCACTTATTAGCTTTTGATAGTAATTATTCAAAAATTT	0	266	0
TTTCTCCCACATCTTTTTAAATCAAAACTCAAACAACAA	1	14	1
TCCCCCCTCTCCCTTTTCTCTTCAACCTTTCTCCATATC	2	31	1
ACTTCTTCCAAGCTTTGAGCATCATCCAACCAGGGGCCT	2	127	1
TTAACTTTTAAGCTTTCTTGAGAAGTTAAGGCTATGAAG	2	219	0
GGTTACAAAGAGCTTTCAGATTCAGAGCTTGAAGCAACT	5	20	1
GATCATGGAAACATTTTAATATCAATGAACCTAATAGTG	8	41	0
CTTAACTTATAAATTTTTCAACAAGAATTTATAAAACTA	9	55	1
          * *****   * **    *
MAP Score: 6.47069