AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_operons032_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944256506
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH0057	134	168aa long hypothetical protein
#1	PH0092	99	821aa long hypothetical phosphoenolpyruvate synthase
#2	PH0093	62	247aa long hypothetical protein
#3	PH0819	221	459aa long hypothetical methyltransferase
#4	PH1001	66	150aa long hypothetical protein
#5	PH1694	31	445aa long hypothetical signal recognition particle protein
#6	PH1701	40	428aa long hypothetical protein
#7	PHS046	224	70aa long hypothetical archaeal histon
#8	PH1875	80	432aa long hypothetical protein

Motif 1
TTTATTGTACACAAACCTTTTAAATGAAAC	0	74	0
TTTGTGTACAATAAACATTTTAAAAATCCC	0	89	1
AAATAGGAATATAAACTTTAAAGGAAAGAA	2	17	0
TTATCCCCGCATAAATTTTTCGAAATTGAA	3	36	1
TGGGCTAAGAACAAATTTTTAGATTACCTC	3	127	1
ATCTGTCCAGATAAATTTTATTTACGAATG	3	169	1
ATGTGGGTTTATAAAGTTTTCGCGAGGAGT	4	18	1
ATGGATGCTTATGAACCTTTACAATAAAGA	7	72	1
GAAAAACTATATAAATTTTTCGGATTTCTC	7	172	0
TTTTGTTTTTATAAACTTATTGTAAACTAT	8	38	1
          **********
MAP Score: 11.6283

Motif 2
TGTACAATAAACATTTTAAAAATCCCCTCTCCC	0	93	1
ACTTAGGGTGAGTTATGGACATTGGAGAACTAA	1	14	1
TATTCACGTTAATTTTAAATATGATCCACCTTT	1	49	1
TCCAGGCTCGAATTTCCGAAATTGATAAAGGTG	1	75	0
TTATATTCCTATTTTTGGATATTTCTTCGGTGC	2	33	1
CCCCGCATAAATTTTTCGAAATTGAATTCATGT	3	40	1
TCATGTGAAGATATTTTAAGAATTTTGCATTTC	3	67	1
CTTAGCCCAGATTTATCGAAATTCATGGGATCC	3	103	0
AATATTCATTAGGTTTTGATATGTCATTCGTAA	3	190	0
TTTCGCGAGGAGTTTTAAACAAGGATAGCGAAA	4	35	1
  GGAAATCTACTTAAAAATAATACTAAAAAAG	6	19	0
GGATTCAATGAATTATAAATAATTGGAGTATTT	7	110	0
TCCAACCAATAGTTTACAATAAGTTTATAAAAA	8	43	0
          * **** ** ***
MAP Score: 9.41976

Motif 3
GATTGATAGTTTCATTTAAAAGGTTTGTGTA	0	66	1
GGTATTCACGTTAATTTTAAATATGATCCAC	1	47	1
GCTCTCTTCTTTCCTTTAAAGTTTATATTCC	2	11	1
CGAAATTGAATTCATGTGAAGATATTTTAAG	3	56	1
TAAAGTAAGATTAACTTGAAGGTGA      	5	16	1
   TGTTTCTTTCTTTTTTAGTATTATTTTT	6	7	1
TTTTTTAGTATTATTTTTAAGTAGATTTCC 	6	20	1
AGCATGTTCTTTATTGTAAAGGTTCATAAGC	7	78	0
TATCAGTCTTTTCATTTCAAAATGGGCGGAA	7	199	0
TTTTATAAACTTATTGTAAACTATTGGTTGG	8	44	1
          ******* ***
MAP Score: 7.62577

Motif 4
ATTTTTAAAATGTTTATTGTACACAAACCTTTT	0	83	0
ACAATAAACATTTTAAAAATCCCCTCTCCCTCT	0	96	1
AGGTGGATCATATTTAAAATTAACGTGAATACC	1	47	0
TACCTTCGGGTATTTATTATCCCCGCATAAATT	3	20	1
TAAGAACAAATTTTTAGATTACCTCTTTGTTAT	3	132	1
TTAGATTACCTCTTTGTTATTCAGATCTGTCCA	3	145	1
TCGCTATCCTTGTTTAAAACTCCTCGCGAAAAC	4	33	0
GTTTCTTTCTTTTTTAGTATTATTTTTAAGTAG	6	11	1
TTGAGCATGTTCTTTATTGTAAAGGTTCATAAG	7	79	0
ATACTCCAATTATTTATAATTCATTGAATCCTT	7	112	1
     CCTTTTATTTATTATCCAACCAATAGTT	8	62	0
          * **** *** **
MAP Score: 6.89131

Motif 5
TATTCCTATTTTTGGATATTTCTTCGGTGCAAG	2	36	1
AAAGAGGTAATCTAAAAATTTGTTCTTAGCCCA	3	127	0
AATGGAAGAATTTGCCAATTTATGGTC      	7	4	0
TACACTAGGTTCTGAACATTTTGTTTTTATAAA	8	20	1
ATCCGAAAAATTTATATAGTTTTTCCGCCCATT	7	177	1
TAAATGTGGGTTTATAAAGTTTTCGCGAGGAGT	4	15	1
GTGAAGATATTTTAAGAATTTTGCATTTCCTGG	3	71	1
ATGATCCACCTTTATCAATTTCGGAAATTCGAG	1	69	1
CTGCTATACCTTCGGGTATTTATTATCCCCGCA	3	14	1
      CCTCTCTGAATATTCATTAGGTTTTGA	3	204	0
ACATTTTGTTTTTATAAACTTATTGTAAACTAT	8	35	1
GAATTCAATTTCGAAAAATTTATGCGGGGATAA	3	36	0
ATAAAATTTATCTGGACAGATCTGAATAACAAA	3	157	0
CTATATAAATTTTTCGGATTTCTCATGCCTGCA	7	163	0
ATATAGTTTTTCCGCCCATTTTGAAATGAAAAG	7	190	1
TAGTATTATTTTTAAGTAGATTTCC        	6	25	1
AATTGGCAAATTCTTCCATTTCTCTTCTTACCT	7	17	1
          **** * **** *
MAP Score: 6.55438

Motif 6
TACCTTAGTTCTCCAATGTCCATAACTCAC	1	21	0
GATCCACCTTTATCAATTTCGGAAATTCGA	1	71	1
   CTCCAGGCTCGAATTTCCGAAATTGAT	1	82	0
CTTCACATGAATTCAATTTCGAAAAATTTA	3	47	0
TTTTAAGAATTTTGCATTTCCTGGGATCCC	3	80	1
CCTGGGATCCCATGAATTTCGATAAATCTG	3	99	1
TTGGCAAATTCTTCCATTTCTCTTCTTACC	7	19	1
GGTTCATAAGCATCCATTTAACCAGTAAAG	7	59	0
ATATAAATTTTTCGGATTTCTCATGCCTGC	7	164	0
CCTATCAGTCTTTTCATTTCAAAATGGGCG	7	202	0
          **********
MAP Score: 5.93872

Motif 7
ATGCCGGCCGTCCCTTTCGCCGCATGATTGATAGTTT	0	41	1
AAAGTTTATATTCCTATTTTTGGATATTTCTTCGGTG	2	28	1
CTTCGGGTATTTATTATCCCCGCATAAATTTTTCGAA	3	23	1
GTCCAGATAAATTTTATTTACGAATGACATATCAAAA	3	173	1
AAAGCAAATTTCGCTATCCTTGTTTAAAACTCCTCGC	4	39	0
    TGTTTCTTTCTTTTTTAGTATTATTTTTAAGTA	6	6	1
ACCAGTAAAGATGCTATCCAGGTAAGAAGAGAAATGG	7	32	0
ATTCATTGAATCCTTATTTGGCCATAATCTCTATGCA	7	130	1
TTGGCCATAATCTCTATGCAGGCATGAGAAATCCGAA	7	147	1
  CCTTTTATTTATTATCCAACCAATAGTTTACAATA	8	55	0
          ** ****    * ** *
MAP Score: 1.82707

Motif 8
TTTTAAAATGTTTATTGTACACAAACCTTTTAAATGAAAC	0	74	0
TCACGTTAATTTTAAATATGATCCACCTTTATCAATTTCG	1	52	1
TCTTCTTTCCTTTAAAGTTTATATTCCTATTTTTGGATAT	2	15	1
TTCACATGAATTCAATTTCGAAAAATTTATGCGGGGATAA	3	36	0
TAAGAACAAATTTTTAGATTACCTCTTTGTTATTCAGATC	3	132	1
CCAGATAAATTTTATTTACGAATGACATATCAAAACCTAA	3	175	1
    TGTTTCTTTCTTTTTTAGTATTATTTTTAAGTAGAT	6	6	1
GAGCATGTTCTTTATTGTAAAGGTTCATAAGCATCCATTT	7	70	0
GTTCTGAACATTTTGTTTTTATAAACTTATTGTAAACTAT	8	28	1
          ***  ***  *    * * *
MAP Score: 0.875786

Motif 9
TATGATCCACCTTTATCAATTTCGGAAATTCGAG	1	68	1
ATATTCCTATTTTTGGATATTTCTTCGGTGCAAG	2	35	1
TCTGCTATACCTTCGGGTATTTATTATCCCCGCA	3	13	1
TTTATTATCCCCGCATAAATTTTTCGAAATTGAA	3	32	1
TGTGAAGATATTTTAAGAATTTTGCATTTCCTGG	3	70	1
TTTCCTGGGATCCCATGAATTTCGATAAATCTGG	3	96	1
TGCTCAAATACTCCAATTATTTATAATTCATTGA	7	105	1
GCATGAGAAATCCGAAAAATTTATATAGTTTTTC	7	168	1
TATATAGTTTTTCCGCCCATTTTGAAATGAAAAG	7	189	1
TTACACTAGGTTCTGAACATTTTGTTTTTATAAA	8	19	1
          *****   **** *
MAP Score: 0.0178547