AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_fusions006_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944254939
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PHS026	300	96aa long hypothetical protein
#1	PH0830	125	319aa long hypothetical protein
#2	PH0840	300	117aa long hypothetical protein
#3	PH0841	47	323aa long hypothetical protein
#4	PH1263	258	320aa long hypothetical protein

Motif 1
ATATTAAGTGAAAGAGTGTGGGATAGTATTCTAAG	0	17	1
AGGTTGAGGAGAAGAATAAAAAAAGTTAATTTTAG	0	89	1
GGCCTCGTAGGAAGAAACGTGGAGAAAAGGAAAGA	0	141	1
GGAGAAAAGGAAAGAGTCAGGAAAGAGGGTTACTT	0	161	1
      CTGGAAAGAGTACTAAAAGATTAGTAGTA	1	4	1
GAGGTCTCTTGAAGATTTTAAAATGTGAAAAGCTT	2	62	1
TGAATGTAAAGAAGAACCTTGAAGATGTGGGGAGT	2	117	1
TGAATTGATGAAAGTTTAGTGAATGAGTCGTTCTG	2	223	0
 GTGCCCTTCAAAGAGTCTGGGATCACGAGTTAAG	3	9	1
AGACACTTCTGAAGAATTGCAGAAGAGAGATTCCC	4	43	1
CCTAATTAAGGAAGATCCAAGGATACTTTCAATTT	4	162	1
   GCTAACTGAAGATCCTAGGAGGATTAGCTTAG	4	236	0
          ***** *   *** *
MAP Score: 16.1016

Motif 2
ATGTAGGATGGGAGGCCCTAAAAGTTCTTCAAGA	0	56	1
GGCCTCGTAGGAAGAAACGTGGAGAAAAGGAAAG	0	141	1
TAGGATTTGGGGAATCCCTTGGAGGCCGCTAGAA	0	200	1
CAGGGAAGCTGAGGTCTCTTGAAGATTTTAAAAT	2	52	1
TGAATGTAAAGAAGAACCTTGAAGATGTGGGGAG	2	117	1
TTGGGAAATTGAGCATCCAAAAAGCCTTAAATAC	2	271	1
TTGCAGAAGAGAGATTCCCTGAAGTTAAGTACTC	4	59	1
AAGTACTCCAGAGAGGACTGGGAGGGGACGTTGC	4	85	1
CCTAATTAAGGAAGATCCAAGGATACTTTCAATT	4	162	1
   GCTAACTGAAGATCCTAGGAGGATTAGCTTA	4	237	0
          ****  **  ****
MAP Score: 14.7915

Motif 3
TATTAAGTGAAAGAGTGTGGGATAGTATTCTA	0	18	1
AGCATGATGTAGGATGGGAGGCCCTAAAAGTT	0	50	1
AAAGTTCTTCAAGAGGTTGAGGAGAAGAATAA	0	76	1
GCCTCGTAGGAAGAAACGTGGAGAAAAGGAAA	0	142	1
GGAAAGAGTCAGGAAAGAGGGTTACTTAGTGT	0	169	1
TACTTAGTGTAGGATTTGGGGAATCCCTTGGA	0	191	1
GCGGATCACAGGGAAGCTGAGGTCTCTTGAAG	2	44	1
AAGAACCTTGAAGATGTGGGGAGTCTCCGTTT	2	128	1
TGGAACCTTCAGGAAACGGAGACTCCCCACAT	2	141	0
ACTGGTCATTGGGAAATTGAGCATCCAAAAAG	2	263	1
GTGCCCTTCAAAGAGTCTGGGATCACGAGTTA	3	10	1
GACACTTCTGAAGAATTGCAGAAGAGAGATTC	4	44	1
TACTCCAGAGAGGACTGGGAGGGGACGTTGCA	4	88	1
CTAATTAAGGAAGATCCAAGGATACTTTCAAT	4	163	1
  GCTAACTGAAGATCCTAGGAGGATTAGCTT	4	238	0
          ****  ******
MAP Score: 12.4946

Motif 4
AAATATTAAGTGAAAGAGTGTGGGATAGTATT	0	15	1
TAATTTTAGTGGAAAAATTAATCTAAGGCCTC	0	115	1
GTGGAGAAAAGGAAAGAGTCAGGAAAGAGGGT	0	159	1
GAAAGAGTCAGGAAAGAGGGTTACTTAGTGTA	0	170	1
        CTGGAAAGAGTACTAAAAGATTAG	1	2	1
GAAAGAGTACTAAAAGATTAGTAGTAGTTATA	1	13	1
GAAAGTTTAGTGAATGAGTCGTTCTGCCTATC	2	217	0
GGTGAATTGATGAAAGTTTAGTGAATGAGTCG	2	228	0
   GTGCCCTTCAAAGAGTCTGGGATCACGAG	3	7	1
ATGCGTTAAGGGAAAGAATAATCATAATTGAT	4	119	1
TTTGAAAAATTGAAAGTATCCTTGGATCTTCC	4	171	0
          *********  *
MAP Score: 9.79606

Motif 5
GGATGGGAGGCCCTAAAAGTTCTTCAAGAG	0	61	1
TTTGGGGAATCCCTTGGAGGCCGCTAGAAA	0	205	1
GATCCCAGTACTTTTGAAGGGTGCTGAGGA	1	82	0
AAGCTGAGGTCTCTTGAAGATTTTAAAATG	2	57	1
GTAAAGAAGAACCTTGAAGATGTGGGGAGT	2	122	1
GAGTCTCCGTTTCCTGAAGGTTCCACGATG	2	148	1
GATCCCAGACTCTTTGAAGGGCAC      	3	4	0
ACTTGAGACACTTCTGAAGAATTGCAGAAG	4	38	1
GAAGAGAGATTCCCTGAAGTTAAGTACTCC	4	64	1
CTCCCAGTCCTCTCTGGAGTACTTAACTTC	4	79	0
TATCAACGCTCCTTTGAAAAATTGAAAGTA	4	185	0
          **********
MAP Score: 6.1706

Motif 6
AAATATTAAGTGAAAGAGTGTGGGATAGTATTCT	0	15	1
ATTCTAAGCATGATGTAGGATGGGAGGCCCTAAA	0	44	1
CTAAAAGTTCTTCAAGAGGTTGAGGAGAAGAATA	0	73	1
GGAAAGAGGGTTACTTAGTGTAGGATTTGGGGAA	0	180	1
CTGGAAAGAGTACTAAAAGATTAGTAGTAGTTAT	1	10	1
  CAGCGAAGTGCGCGTGTATGAGCTTATCCCTT	2	8	1
TATGCGGATCACAGGGAAGCTGAGGTCTCTTGAA	2	41	1
TTAGGTGAATTGATGAAAGTTTAGTGAATGAGTC	2	229	0
   GTGCCCTTCAAAGAGTCTGGGATCACGAGTT	3	7	1
GAAGAGAGATTCCCTGAAGTTAAGTACTCCAGAG	4	64	1
TGGATCTTCCTTAATTAGGTTTGGGAACTCATCA	4	147	0
          * *  **** ****
MAP Score: 0.916151

Motif 7
AGTTCTTCAAGAGGTTGAGGAGAAGAATAA	0	78	1
ACTTAGTGTAGGATTTGGGGAATCCCTTGG	0	192	1
GCTAGAAACAGTAAATGTGGATAGCTGTAA	0	227	1
ACTTTTGAAGGGTGCTGAGGAATCCTTTCT	1	73	0
CGAAGTGCGCGTGTATGAGCTTATCCCTTA	2	13	1
GGATCACAGGGAAGCTGAGGTCTCTTGAAG	2	46	1
GAAGAACCTTGAAGATGTGGGGAGTCTCCG	2	127	1
TGAAAGTTTAGTGAATGAGTCGTTCTGCCT	2	220	0
TGGTCATTGGGAAATTGAGCATCCAAAAAG	2	265	1
TTATTATTTAGCTGTTGAGGGAGACAACTT	4	12	1
GATTAGCTTAGTGTTTGAGTTTGACAAGTC	4	217	0
          **********
MAP Score: 0.613641