AlignACE 3.0 10/20/99
AlignACE2 -i PA/PA_fusions003_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944248417
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PAB2043	72	PAB2043
#1	PAB2042	35	hypothetical protein
#2	PAB2041	55	hypothetical protein
#3	PAB2040	69	PAB2040
#4	PAB2039	124	hypothetical protein
#5	PAB0547	300	hypothetical protein

Motif 1
AAAACCTTTATATACTTCTCCTTTTCTAGA	2	14	1
         TTCTTCTTCTTTTTTAAACAA	3	1	1
GAAAGAAGCTTCAAGTTCTCTCGATTAACT	4	58	1
CTAACTCAATTCATCTTCACAACTTTTAAA	4	87	0
CTACTAAAGATCTACTTCACAATATTACAT	5	55	0
AGGAGACAACTCAACTTCTTTTCCCAAAGT	5	193	1
          **********
MAP Score: 6.45745

Motif 2
CCAGATATACCGGTCCAAACTCTTAAATTTGAAGTTAGATTTT	0	15	1
CCTTTATATACTTCTCCTTTTCTAGATTCTTTATAATTTCCGC	2	18	1
ATCACCATGAACAAATATGCCCTGAAATATTTAAGCCATTTTA	4	14	1
TCGCCTAACTCAATTCATCTTCACAACTTTTAAAGTTAATCGA	4	78	0
TGCATGAATTAAAAACTTTACCTTGTTTATGTAATATTGTGAA	5	27	1
TTTAGACTTGCATGACTTATCCTGATCTTTGGAGTTATATGTT	5	136	1
GAGACAACTCAACTTCTTTTCCCAAAGTAAGGAAATTTAAACC	5	195	1
ATTTAAACCCAACACCCTATCCATTATTTTGCATGTATATGTT	5	229	1
          *    * *  **   * * ** *
MAP Score: 3.16221

Motif 3
      GAACCTTTTTATTCCCTCCCTCACTCT	1	4	1
CCTTTATATACTTCTCCTTTTCTAGATTCTTTA	2	18	1
        TTCTTCTTCTTTTTTAAACAATAAA	3	2	1
ATGAAAGAAGCTTCAAGTTCTCTCGATTAACTT	4	56	1
GAATTAAAAACTTTACCTTGTTTATGTAATATT	5	32	1
ACTTGCATGACTTATCCTGATCTTTGGAGTTAT	5	141	1
          *** * *** ***
MAP Score: 2.28193

Motif 4
          GGTGGCCAGATATACCGGTCCAA	0	0	1
TTAGCTTCTTGGTGGGCTTAAATGG        	0	57	1
AGAGAGTGAGGGAGGGAATAAAAAGGTTC    	1	6	0
AATTGAGTTAGGCGAGCCGAAATTTGGG     	4	106	1
TGGATAGGGTGTTGGGTTTAAATTTCCTTACTT	5	219	0
          ** ***  *****
MAP Score: 1.39769

Motif 5
TGAAGTTAGATTTTTAGCTTCTTGGTGGGCTTA	0	44	1
      GAACCTTTTTATTCCCTCCCTCACTCT	1	4	1
CCTTTATATACTTCTCCTTTTCTAGATTCTTTA	2	18	1
TTCTAGATTCTTTATAATTTCCGCATTC     	2	37	1
        TTCTTCTTCTTTTTTAAACAATAAA	3	2	1
ATCGAGAGAACTTGAAGCTTCTTTCATAAAATG	4	50	0
CAAGGTAAAGTTTTTAATTCATGCATTTCTACA	5	19	0
AGTATGTCAGTTTGTGGCTCTCTGCTGAATTCT	5	83	1
GGGTGTTGGGTTTAAATTTCCTTACTTTGGGAA	5	213	0
TTGACCGATTTTTAAGGTTTATTTTAACATATA	5	264	0
          *** *  ******
MAP Score: 0.523558