AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_fusions002_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944254898
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH1516	149	303aa long hypothetical dihydroorotate dehydrogenase
#1	PH1517	93	460aa long hypothetical protein
#2	PH1739	113	212aa long hypothetical protein

Motif 1
      TATTTTATCTCCCTCTATCAGGATA	0	4	1
TCTATCAGGATATCAGCCCTAGTTGGATGAT	0	23	1
TGATACCAGCTATCATCCAACTAGGGCTGAT	0	34	0
          TTTTATCCCTCCCAGGATCTT	1	82	0
          TTTCTTCCCTAGTCCTTTTCT	2	0	1
CCCTAGTCCTTTTCTACCCTATCCTTCATAA	2	16	1
TTAAAAGGATTTCCATCCACCCGGAACCTTT	2	45	0
          TTCACTCCCCCCAATTAGCTT	2	102	0
          **** ******
MAP Score: 6.516

Motif 2
TATTTTATCTCCCTCTATCAGGATATCAGCCCTAG	0	10	1
GGATATCAGCCCTAGTTGGATGATAGCTGGTATCA	0	30	1
GATAAGGCCTCCCTTTAATAGAATTGACAAGTCAG	0	70	1
AGTCAGATCACCTAATTTTAGAATTACAGTTTAAT	0	99	1
AATATAAAAACCTTATTTGAAACTTTGA       	0	131	1
CCACCCGGAACCTTTATGAAGGATAGGGTAGAAAA	2	25	0
ATATTTTTAACTAGTTAAAAGGATTTCCATCCACC	2	55	0
          **   **  ******
MAP Score: 3.57222

Motif 3
TCAATTCTATTAAAGGGAGGCCTTATCTTA	0	67	0
AATGGAAAGATCCTGGGAGGGATAAAA   	1	76	1
GATATCCTGATAGAGGGAGATAAAATA   	0	7	0
AATGTCAAGCTAATTGGGGGGAGTGAA   	2	96	1
ATATCAGCCCTAGTTGGATGATAGCTGGTA	0	32	1
ATTATCGACATAATGAGACGGGAAAAGTTA	1	24	1
          **********
MAP Score: 2.70933

Motif 4
CTGATATCCTGATAGAGGGAGATAAAATA 	0	9	0
CAATTCTATTAAAGGGAGGCCTTATCTTAT	0	66	0
AAAAATCAAAAATGGAAAGATCCTGGGAGG	1	66	1
TGGAAAGATCCTGGGAGGGATAAAA     	1	78	1
TAGAAAAGGACTAGGGAAGAAA        	2	2	0
TTTATGAAGGATAGGGTAGAAAAGGACTAG	2	18	0
AAAGGTTCCGGGTGGATGGAAATCCTTTTA	2	45	1
TGTCAAGCTAATTGGGGGGAGTGAA     	2	98	1
          **********
MAP Score: 1.40325

Motif 5
   TATTTTATCTCCCTCTATCAGGATATCAGCCCTA	0	7	1
TATCAGGATATCAGCCCTAGTTGGATGATAGCTGGTA	0	25	1
ATGTTATAACTTTTCCCGTCTCATTATGTCGATAATA	1	23	0
CCTCCCAGGATCTTTCCATTTTTGATTTTTCGACAAA	1	59	0
        TTTCTTCCCTAGTCCTTTTCTACCCTATC	2	2	1
CTAGTCCTTTTCTACCCTATCCTTCATAAAGGTTCCG	2	18	1
          *** *** * **    *
MAP Score: 0.247309

Motif 6
ATCCTGATAGAGGGAGATAAAATA       	0	3	0
TATCAGCCCTAGTTGGATGATAGCTGGTATC	0	33	1
GACATAATGAGACGGGAAAAGTTATAACATT	1	30	1
GAAAAATCAAAAATGGAAAGATCCTGGGAGG	1	65	1
AAAGATCCTGGGAGGGATAAAA         	1	81	1
ATGAAGGATAGGGTAGAAAAGGACTAGGGAA	2	14	0
TAAAGGTTCCGGGTGGATGGAAATCCTTTTA	2	44	1
CAAGCTAATTGGGGGGAGTGAA         	2	101	1
          ** ********
MAP Score: 0.0973248