AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_fusions012_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944255050
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH0507	300	321aa long hypothetical oligopeptide transport ATP-binding protein AppF
#1	PH0807	174	597aa long hypothetical oligopeptide binding protein APPA
#2	PH0808	41	323aa long hypothetical oligopeptide transport permease protein APPB
#3	PH0820	221	312aa long hypothetical ATP-binding protein
#4	PH1815	24	284aa long hypothetical cobalt transport ATP-binding protein

Motif 1
CGGGTGAGCTGGAGATTCTAGAACCTCCTCCA	0	58	0
ATTCTCGGGAGAGAATTCAAAAGGAGTTGAGT	0	93	0
CAACCCTCAGGAGGATTCAAGAGACTAATCGG	0	171	0
TTGTCGAATTGAAAGTCCAAAACT        	1	2	0
ATTTGGCATTGAAGATCATAGATTCTCAAGAT	1	80	0
ACAAAGAAAAGGGGAATAAAAATAAAAA    	2	6	0
TTTCTTTGTTGGAGGTGAGAGA          	2	29	1
TGGGATCCCAGGAAATGCAAAATTCTTAAAAT	3	130	1
AAATTTATGCGGGGATAATAAATACCCGAAGG	3	187	1
          ****** * ***
MAP Score: 8.38811

Motif 2
       ATAGGGTGATGATTATGTACGCTGGGAAGGTT	0	3	1
ACGCTGGGAAGGTTGTTGAGATTGGAAGCATGGAGGAGG	0	28	1
TGTACGGGTGAGCTGGAGATTCTAGAACCTCCTCCATGC	0	55	0
TCCTCCTGAGGGTTGTAGGTTTTATACTCGTTGTCCTTA	0	188	1
          AGTTTTGGACTTTCAATTCGACAAATTTA	1	0	1
TGCATTAGTGATATGTTAAAATTTAACCCTATATTTTTG	1	41	0
CACTAATGCAATCTTGAGAATCTATGATCTTCAATGCCA	1	70	1
AATATTCATTAGGTTTTGATATGTCATTCGTAAATAAAA	3	18	1
AATTGAATTCATGTGAAGATATTTTAAGAATTTTGCATT	3	143	0
CCCCGCATAAATTTTTCGAAATTGAATTCATGTGAAGAT	3	162	0
CGAAAAATTTATGCGGGGATAATAAATACCCGAAGGTAT	3	183	1
          ** **  ** * *  *  *
MAP Score: 6.97247

Motif 3
ATGGAGGAGGTTCTAGAATCTCCAGCTCACCC	0	57	1
ACTCAACTCCTTTTGAATTCTCTCCCGAGAAT	0	93	1
GGGAGAGGCTTCGTGGGATTCCTGGTTACCCG	0	142	1
CCGATTAGTCTCTTGAATCCTCCTGAGGGTTG	0	171	1
        AGTTTTGGACTTTCAATTCGACAA	1	2	1
GCATTGAAGATCATAGATTCTCAAGATTGCAT	1	75	0
AAGAACAAATTTTTAGATTACCTCTTTGTTAT	3	76	0
TTATCGAAATTCATGGGATCCCAGGAAATGCA	3	117	1
ATTTTAAGAATTTTGCATTTCCTGGGATCCCA	3	130	0
AATGCAAAATTCTTAAAATATCTTCACATGAA	3	143	1
          ** **** ****
MAP Score: 6.54794

Motif 4
AGGAGGTTCTAGAATCTCCAGCTCACCCGTA	0	61	1
CTCCTTTTGAATTCTCTCCCGAGAATGGGTG	0	99	1
AATCCCACGAAGCCTCTCCCTCTTATAATGA	0	131	0
CGGGTAACCAGGAATCCCACGAAGCCTCTCC	0	143	0
AATTAGTTGAAGTTTCCCCAGGGCATTACGC	0	259	1
TGAAGATCATAGATTCTCAAGATTGCATTAG	1	72	0
TGCATTTCCTGGGATCCCATGAATTTCGATA	3	118	0
         GATGCTCCCAAGGAGAGGGGAG	4	1	1
          ** ********
MAP Score: 5.48663

Motif 5
TGTACGCTGGGAAGGTTGTTGAGATTGGAAGCATGGAGGAG	0	25	1
GTTGAGATTGGAAGCATGGAGGAGGTTCTAGAATCTCCAGC	0	42	1
ATAAGAGGGAGAGGCTTCGTGGGATTCCTGGTTACCCGATT	0	136	1
CAACCCTCAGGAGGATTCAAGAGACTAATCGGGTAACCAGG	0	162	0
GAATCCTCCTGAGGGTTGTAGGTTTTATACTCGTTGTCCTT	0	185	1
ATGCAATCTTGAGAATCTATGATCTTCAATGCCAAATTCCG	1	75	1
TTTTAAGATTTAAAATTGGGGGTAATCTTAG          	1	153	1
GTTCTTAGCCCAGATTTATCGAAATTCATGGGATCCCAGGA	3	102	1
TTCATGTGAAGATATTTTAAGAATTTTGCATTTCCTGGGAT	3	134	0
TATCCCCGCATAAATTTTTCGAAATTGAATTCATGTGAAGA	3	163	0
          **** **   **   *    *
MAP Score: 4.76178

Motif 6
CAGCGTACATAATCATCACCCTAT      	0	4	0
ATGCTTCCAATCTCAACAACCTTCCCAGCG	0	29	0
TCACCCGTACACTCAACTCCTTTTGAATTC	0	83	1
TCCCTCTTATAATGAACACCCATTCTCGGG	0	116	0
        TCTCTCACCTCCAACAAAGAAA	2	29	0
ACGAATGACATATCAAAACCTAATGAATAT	3	19	0
          **********
MAP Score: 2.05059