AlignACE 3.0 10/20/99
AlignACE2 -i PA/PA_fusions009_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944248651
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	ileS	250	PAB0616
#1	PAB1727	83	hypothetical protein
#2	PAB0660	116	hypothetical protein
#3	metS	73	PAB2364
#4	cysS	116	PAB0931

Motif 1
ATGATAAATAGATCCCCCCTCATTAGCATCGC	0	158	0
      TTTACCTCCCCCCACATGTCTTAACC	3	57	0
CTTTTGAAAGCCTCGCCCCTCAGCGCGGGGGG	0	54	0
CTTTTCCTTGGACCCCCCCGCGCTGAGGGGCG	0	41	1
          GTCCTCCCCCTGGCTAAAATCG	4	104	0
AGGAAGTTAGGATAGCCCCCAACT        	2	2	0
CCCTCATTAGCATCGCCCAAAGTTGGGATGAG	0	142	0
          * ******* **
MAP Score: 8.34243

Motif 2
GAACTACAACTTCAATCAAGGTTCTATACTTAT	0	85	1
TCCTATGAGCTCAAATTAAGGTCTTCCTCTTCT	0	189	1
GGTTAGCTACTTCTATAAACGTCTGGAGGGTTC	0	223	1
AAAATTGGCGTTTAATAAAGGTTTGGTAAAATG	1	20	1
ATATATATGGTTTAATTTAAGTTAGAATCGGTG	1	53	1
ATGTTTAAATTTGCCTTCAGGTTAAGACATGTG	3	38	1
AAACGTTGCTTTCTCTTAAGGTTGCCAAAACCG	4	49	1
          **  ** ******
MAP Score: 4.99136

Motif 3
CAAAAGAACTACAACTTCAATCAAGGTTCTATACTTAT	0	80	1
TATCATCCTATGAGCTCAAATTAAGGTCTTCCTCTTCT	0	184	1
TAGGGAAAATTGGCGTTTAATAAAGGTTTGGTAAAATG	1	15	1
AAATGATATATATGGTTTAATTTAAGTTAGAATCGGTG	1	48	1
TCGTAATGTTTAAATTTGCCTTCAGGTTAAGACATGTG	3	33	1
TATTTAAACGTTGCTTTCTCTTAAGGTTGCCAAAACCG	4	44	1
          *    **  **  *****
MAP Score: 1.64265

Motif 4
ACTTTTCCTTGGACCCCCCCGCGCTGAGGG	0	40	1
TTTTGAAAGCCTCGCCCCTCAGCGCGGGGG	0	55	0
AATCTTATAAGTTCTCATCCCAACTTTGGG	0	129	1
CCCCCTCATTAGCATCGCCCAAAGTTGGGA	0	146	0
TGATAAATAGATCCCCCCTCATTAGCATCG	0	159	0
       TTCAGAACCCTCCAGACGTTTAT	0	237	0
AAGTTAGGATAGCCCCCAACT         	2	1	0
        TAATATTCACCCATAATAACCC	3	2	1
ATATTCACCCATAATAACCCTTCGTAATGT	3	12	1
     TTTACCTCCCCCCACATGTCTTAAC	3	58	0
GTCTAATAAGAGAATACCCCGATTTTAGCC	4	85	1
          GTCCTCCCCCTGGCTAAAAT	4	106	0
          **********
MAP Score: 0.547776