AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_operons009_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944255650
 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
TAAAAACTCTCAAACCTTTTCCAAAAATAT	0	46	1
TAACTTTTTACAAAAATTAAATAAAAACTC	0	25	1
AAACCTTTTCCAAAAATATATCCTCCTCAA	0	57	1
CTTTTTAAATCAAAACTCAAACAACAATTC	1	26	1
AATTTTTCAACAAGAATTTATAAAACTAGA	9	66	1
TGAGATCATGGAAACATTTTAATATCAATG	8	53	0
TTAAGTAAGTCAAGACTCTTATATACCTTC	8	121	0
TCTGTTCTGGGAAAACTAAACCATCGGG  	4	63	1
CTCTGAATCTGAAAGCTCTTTGTAACCCTC	5	17	0
AACTTCTCAAGAAAGCTTAAAAGTTAACTC	2	231	1
GCCAAAAATCCAAAAATAATCCCAAATATC	0	226	1
GAGTAGCTTGGAAGCCTATTCTGTAATAAT	2	89	1
CTATGAAGGCCAAGGATATAGTTCTCAAAA	2	197	0
          **********
MAP Score: 14.8621

Motif 2
TAAATAAAATATTGAGGAGGATATATTTTT	0	68	0
AAGAGAAAAGGGAGAGGGGGGAAGAGATCA	2	23	0
ATGGAGAAAGGTTGAAGAGAAAAGGGAGAG	2	37	0
GCTACTCACCTGGGAAGGGCCATAGAGATA	2	66	0
AAGCGAGAAAATTGAAGGGGTTGAAGTTAA	2	166	0
AAATTCTCAAGGGGAAGTGGAGGAAATGGA	4	29	0
ACTCTCAAGCAGTGAGAGGGAG        	5	56	1
TCGTAGTTATATTGAGGGGGTTCTTAGACC	6	28	0
ATTTTTCCTTTTTGTGGGGGTGAAACC   	7	10	1
CTTTAATGGCGGTGATGGGCC         	8	1	0
CTTACTTAAGGTGGAGGTGAGAAG      	8	142	1
TAATGTAGTGTGAGAAGGGGGTTATAGGAG	9	10	0
GATTTTCTCTGGTGAGGTGGT         	9	101	1
          **********
MAP Score: 12.856

Motif 3
ATAAAATATTGAGGAGGATATATTTTTGGA	0	65	0
TTAAAAAGATGTGGGAGAAAAGTT      	1	4	0
  TTGGGCACGGGGAAGAACTGAATTGTTG	1	47	0
AAGGGAGAGGGGGGAAGAGATCAGAGTATT	2	16	0
ATGGAGAAAGGTTGAAGAGAAAAGGGAGAG	2	37	0
GCCCTTCCCAGGTGAGTAGCTTGGAAGCCT	2	76	1
AATTGAAGGGGTTGAAGTTAAAGGCCCCTG	2	157	0
ATCGGCGTTTGGGGAGTTAACTTTTAAGCT	2	244	0
CCCAAACGCCGATGGGGAGCGAACC     	2	261	1
TCAAGGGGAAGTGGAGGAAATGGAGTATAT	4	23	0
TAGTTATATTGAGGGGGTTCTTAGACCGCC	6	25	0
TTTCCTTTTTGTGGGGGTGAAACC      	7	13	1
CTTACTTAAGGTGGAGGTGAGAAG      	8	142	1
GATTTTCTCTGGTGAGGTGGT         	9	101	1
          **********
MAP Score: 12.3146

Motif 4
GAAAAGTACTAACTTTTTACAAAAATTAAATAAA	0	16	1
AAAACTCTCAAACCTTTTCCAAAAATATATCCTC	0	48	1
AAAATTTTTGAAATTTTTAAATAAAATATTGAGG	0	81	0
AAATTTCAAAAATTTTCGTAACAATTTAATAACA	0	99	1
TTTAATAACAAAACTTTAACATAAGGAAAATACT	0	123	1
GTCTAGGCTTAATTTTTAGAATAGAGGTTTTAGA	0	189	0
TTGCACCGAAAAATTTTTGAATAATTACTATCAA	0	256	1
          AACTTTTCTCCCACATCTTTTTAA	1	0	1
TTCATAGCCTTAACTTCTCAAGAAAGCTTAAAAG	2	220	1
CCCGATGGTTTAGTTTTCCCAGAACAGAAGAAAA	4	57	0
CTAATCTATTAACTTTTCTCCCAGGAAGTCATCA	6	118	0
CTTAACTTATAAATTTTTCAACAAGAATTTATAA	9	55	1
          ** ****  ** **
MAP Score: 11.0882

Motif 5
TAAATAAAAACTCTCAAACCTTTTCCAAAAATA	0	42	1
GGGCCTTTAACTTCAACCCCTTCAATTTTCTCG	2	160	1
TTCTCCATATCTCTATGGCCCTTCCCAGGTGAG	2	59	1
ACTTTATATACTCCATTTCCTCCACTTCCCCTT	4	18	1
CTAAGTCAAACTCTAATCCCTCTAAAACCTCTA	0	169	1
ATACTCTGATCTCTTCCCCCCTCTCCCTTTTCT	2	17	1
TCTCCCTTTTCTCTTCAACCTTTCTCCATATCT	2	38	1
TCTGAAAGCTCTTTGTAACCCTCCTTTGTT   	5	7	0
   AACTTTTCTCCCACATCTTTTTAAATCAAA	1	7	1
AGTCAAGACTCTTATATACCTTCCGCGAGAGCA	8	111	0
TGAGAACTATATCCTTGGCCTTCATAGCCTTAA	2	200	1
       CTCCTATAACCCCCTTCTCACACTAC	9	3	1
GGGGAGTTAACTTTTAAGCTTTCTTGAGAAGTT	2	231	0
CGCCGGCGGTCTAAGAACCCCCTCAATATAACT	6	21	1
          **** *  *****
MAP Score: 8.97234

Motif 6
    AACTTTTCTCCCACATCTTTTTAAATC	1	6	1
AATACTCTGATCTCTTCCCCCCTCTCCCTTT	2	16	1
GCCTTTAACTTCAACCCCTTCAATTTTCTCG	2	162	1
      CTACACACCCCCGCCGGCGGTCTAA	6	4	1
      GGTTTCACCCCCACAAAAAGGAAAA	7	12	0
      CTTCTCACCTCCACCTTAAGTAAGT	8	141	0
    CTCCTATAACCCCCTTCTCACACTACA	9	6	1
          ******** **
MAP Score: 6.09131

Motif 7
GTTTTTATTTAATTTTTGTAAAAAGTTAGTACTTTTC	0	16	0
AAAAACTCTCAAACCTTTTCCAAAAATATATCCTCCT	0	47	1
ATCCTCCTCAATATTTTATTTAAAAATTTCAAAAATT	0	76	1
AAAATTTCAAAAATTTTCGTAACAATTTAATAACAAA	0	98	1
CTTGCACCGAAAAATTTTTGAATAATTACTATCAAAA	0	255	1
TTTTCTCTTCAACCTTTCTCCATATCTCTATGGCCCT	2	44	1
GTTAACTTTTAAGCTTTCTTGAGAAGTTAAGGCTATG	2	222	0
TAGTTTTATAAATTCTTGTTGAAAAATTTATAAGTTA	9	57	0
          **  *** *  * ** *
MAP Score: 4.29428

Motif 8
AAGAAAAGTACTAACTTTTTACAAAAATTAAATAAAAAC	0	14	1
AAAAACTCTCAAACCTTTTCCAAAAATATATCCTCCTCA	0	47	1
AAAATTTTTGAAATTTTTAAATAAAATATTGAGGAGGAT	0	76	0
AAAAATTTCAAAAATTTTCGTAACAATTTAATAACAAAA	0	97	1
ATTTAATAACAAAACTTTAACATAAGGAAAATACTAATT	0	122	1
AATCCCTCTAAAACCTCTATTCTAAAAATTAAGCCTAGA	0	183	1
AATTATTCAAAAATTTTTCGGTGCAAGATATTTGGGATT	0	243	0
TAACCACTTATTAGCTTTTGATAGTAATTATTCAAAAAT	0	268	0
CTTTTCTCTTCAACCTTTCTCCATATCTCTATGGCCCTT	2	43	1
AGTTAACTTTTAAGCTTTCTTGAGAAGTTAAGGCTATGA	2	221	0
     AATCGAAAACTTTATATACTCCATTTCCTCCACT	4	5	1
AAAGGTATATAAACCTTTTGTGTTACTATCTAGAGTTAG	6	64	1
GGCTAATCTATTAACTTTTCTCCCAGGAAGTCATCAAAA	6	115	0
AACTGAGAGATAATCTCTTAACTTATAAATTTTTCAACA	9	39	1
          *** ****      *  **
MAP Score: 2.03744