AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_fusions010_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944255003
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH0502	151	641aa long hypothetical protein
#1	PH0503	35	330aa long hypothetical oligopeptide transport system permease protein AppB
#2	PH1408	233	226aa long hypothetical protein
#3	PH1409	250	721aa long hypothetical protein
#4	PH1410	117	332aa long hypothetical dipeptide transport system permease protein dppB

Motif 1
       TCAATCTCCCCCTCATCATGTTA	0	3	1
TGTTTTTATAACTTCCCTTAAATCTGAATT	0	46	1
ATCTGAATTAATCCCCCCTTTTAATCCTCA	0	67	1
         GCTCTCTCTTTTATTATTTTG	1	1	1
       AATATTCCCCCCAACAAAATAAT	1	22	0
ATAGGCGTACATCTCTCTTTCCTCGAGGAT	2	38	0
CCCTTTCTATATGCCTCCTTTATGAGGCCT	2	142	0
AATATATCCTCTTCCCCTTTCTATATGCCT	2	156	0
TAAGCCTTCTACCTCTCTCAGTCAGCTTGT	2	186	0
        TCACCACCCTCTACTCAAGATT	2	221	0
ACATTCAAAAACATCTCTCTAATTCCCTTA	3	69	1
GTGCCTGGTTATATCTCTTTGGATAACCTT	3	215	1
 TAATCTTTCTTCTCTCTTTTCTTTATTGC	4	9	1
      ATTTGCCCCTCCTTGTACATTCTT	4	103	0
          **********
MAP Score: 10.4348

Motif 2
CCCCCTTTTAATCCTCAAGCTAATTATAAT	0	80	1
GGATTTTAAGAATCTCAAGCTTAGTTCCAC	2	12	0
GATTCTTAAAATCCTCGAGGAAAGAGAGAT	2	28	1
AAACCCCTAAAGTATCAAGCCGTTCATCAG	2	89	1
ATTTTTAAGCATCTTCAAGGTGAAACAATA	3	13	0
TACACCACTGATTTTTAAGCATCTTCAAGG	3	23	0
CGATAATATAATTCTCAAACGATGTTATAG	4	70	1
          **********
MAP Score: 3.95177

Motif 3
GAATTAATCCCCCCTTTTAATCCTCAAGCTAATTATAA	0	71	1
AATCCTCAAGCTAATTATAATCAAAAAGTTTATATAAT	0	89	1
ATAATGTGAACTTCTTATAAAAATTGAGTCTTAATTAT	0	122	1
TAAGCTTGAGATTCTTAAAATCCTCGAGGAAAGAGAGA	2	19	1
AGGTAGAAGGCTTATTGAAAATCTTGAGTAGAGGGTGG	2	202	1
         GCTTATTGTTTCACCTTGAAGATGCTTAA	3	1	1
CACCTTGAAGATGCTTAAAAATCAGTGGTGTATCATTT	3	21	1
AATTTTATTACTAATTGTTATAATTTGGATCTTCTATT	3	137	1
AGCGAGGTGCCTGGTTATATCTCTTTGGATAACCTTCC	3	209	1
CTTTATTGCCCTTATTTAAACACCAAAATTTTTATTTA	4	30	1
CTTGTACATTCTTGTTCTATAACATCGTTTGAGAATTA	4	78	0
          **  ** ***  *   **
MAP Score: 3.86289

Motif 4
AGGTAGAAGGCTTATTGAAAATCTTGAGTA	2	202	1
ATGTGAACTTCTTATAAAAATTGAGTCTTA	0	125	1
ATAAAGGAGGCATATAGAAAGGGGAAGAGG	2	149	1
TTTAAGGGAAGTTATAAAAACATTCAAATT	0	38	0
CTCAAACGATGTTATAGAACAAGAATGTAC	4	83	1
CTTTATTGCCCTTATTTAAACACCAAAATT	4	30	1
AGAAGTTCACATTATATAAACTTTTTGATT	0	107	0
          **********
MAP Score: 3.71962

Motif 5
    TCAATCTCCCCCTCATCATGTTACTG	0	6	1
TTTTATAACTTCCCTTAAATCTGAATTAAT	0	49	1
TCTGAATTAATCCCCCCTTTTAATCCTCAA	0	68	1
      GCTCTCTCTTTTATTATTTTGTTG	1	4	1
     AATATTCCCCCCAACAAAATAATAA	1	20	0
TAGGCGTACATCTCTCTTTCCTCGAGGATT	2	37	0
CCTTTCTATATGCCTCCTTTATGAGGCCTA	2	141	0
TAATATATCCTCTTCCCCTTTCTATATGCC	2	157	0
TTCAAAAACATCTCTCTAATTCCCTTATTT	3	72	1
TAATCTTTCTTCTCTCTTTTCTTTATTGCC	4	10	1
TTTTCTTTATTGCCCTTATTTAAACACCAA	4	26	1
       ATTTGCCCCTCCTTGTACATTCT	4	104	0
          **********
MAP Score: 3.3473

Motif 6
ATCCTCGAGGAAAGAGAGATGTACGCCTATGAA	2	38	1
AAGGAGGCATATAGAAAGGGGAAGAGGATATAT	2	152	1
TTACAAGCTGACTGAGAGAGGTAGAAGGCTTAT	2	184	1
GATGCTTAAAAATCAGTGGTGTATCATTTTGAT	3	30	1
AGGGAAGGTTATCCAAAGAGATATAACCAGGCA	3	216	0
GCAATAAAGAAAAGAGAGAAGAAAGATTA    	4	6	0
AAGAATGTACAAGGAGGGGCAAAT         	4	103	1
          *  ****** ***
MAP Score: 1.6783