AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_fusions002_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944254903
 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
  TATTTTATCTCCCTCTATCAGGATATCA	0	8	1
AAGATAAGGCCTCCCTTTAATAGAATTGAC	0	68	1
CCCTCCCAGGATCTTTCCATTTTTGATTTT	1	67	0
      TTTTATCCCTCCCAGGATCTTTCC	1	79	0
TTCTTCCCTAGTCCTTTTCTACCCTATCCT	2	11	1
GTGGATGGAAATCCTTTTAACTAGTTAAAA	2	56	1
      TTCACTCCCCCCAATTAGCTTGAC	2	99	0
          **********
MAP Score: 4.00013

Motif 2
AACTAGGGCTGATATCCTGATAGAGGGAGATAAAATA      	0	4	0
TCGAAGTTATTATCGACATAATGAGACGGGAAAAGTTATAACA	1	16	1
AAATCAAAAATGGAAAGATCCTGGGAGGGATAAAA        	1	68	1
ACCCGGAACCTTTATGAAGGATAGGGTAGAAAAGGACTAGGGA	2	15	0
CTATCCTTCATAAAGGTTCCGGGTGGATGGAAATCCTTTTAAC	2	34	1
TTTAACTAGTTAAAAATATTTGGTAAATGTCAAGCTAATTGGG	2	71	1
TTGGTAAATGTCAAGCTAATTGGGGGGAGTGAA          	2	90	1
          *  *   *   ** **  *  **
MAP Score: 1.47689