AlignACE 3.0 10/20/99
AlignACE2 -i PA/PA_fusions002_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944248389
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	sucC-like	166	PAB0203
#1	PAB2112	133	PAB2112
#2	PAB1937	93	hypothetical protein
#3	PAB1936	49	PAB1936
#4	ftsZ-2	300	PAB0851
#5	soj	48	PAB0852
#6	PAB0854	99	hypothetical protein
#7	PAB1431	51	hypothetical protein

Motif 1
AACATTTGAGAGAAAGATATCCGCAACCCTTGAGTC	0	59	1
TAGTCTTACTTAAAAGTTTTATGAAAAGGAGATCAT	1	54	0
AAAACTGAAAATTAAATTAGAGGTGATACTC     	1	112	1
GTCATTATCGACAAAAAAAGACGGGAAAGGTTATAA	2	21	1
GGGAAAGGTTATAACATTTGTCGAAAATCAAAAATT	2	43	1
TTGTCGAAAATCAAAAATTGAAGCGAATTTGGGAGG	2	60	1
    CAGCTAAAGAACATCGATGAAATATAAAAACC	3	6	1
ATGAAATATAAAAACCTTATTTGAGAAGTCGAG   	3	26	1
TAGGCCATGAATTAAATTCTGGGGAAGTTGGACGCT	4	123	0
AATTTATCTAACAACGTATTCGGGGATTTCTTCCTG	4	258	0
ACGTTGTTAGATAAATTTTGGGGGGAGTGAAAG   	4	277	1
TTCATCACCTAAAAAGAAGTGGGAAAGGAAATTTTA	5	22	0
TTGATGTTCAAGAAATAAATTAGTGAAA        	6	2	0
          * *** ** *  * **
MAP Score: 9.95607

Motif 2
TTGGGCTCGATACTATAAATATTTAATGGTTTAGAT	0	22	1
ATTTAATGGTTTAGATGAACATTTGAGAGAAAGATA	0	42	1
ATCATCAAACGGACAAAAGGTTTTAAATTAACTCCA	1	23	0
ATGATCTCCTTTTCATAAAACTTTTAAGTAAGACTA	1	54	1
ATTTTTGATTTTCGACAAATGTTATAACCTTTCCCG	2	42	0
 CTCGACTTCTCAAATAAGGTTTTTATATTTCATCG	3	24	0
    ATATTATCACAAAAATAATTTAGGCCAAAAAG	4	6	1
AAATAATTTAGGCCAAAAAGTATTTAACTAATTAAA	4	22	1
GATTCTCTTGTTAAAAGAGGTATTTATCCGAATAGA	4	159	1
AAAAGAAGTGGGAAAGGAAATTTTAAAGTTTAAAGT	5	11	0
TACATTGATGTTCAAGAAATAAATTAGTGAAA    	6	6	0
AGGATCAAGGTCTAAGAAATCTTATAAGATCGCTTA	6	50	1
TTATAAGATCGCTTAGGAAGCATTTACTGGTGAAGC	6	71	1
          *   * ***  *****
MAP Score: 7.65185

Motif 3
AAAAGCATGGAAATACTTTTAACCACTTCG	0	108	1
GGAGTTAATTTAAAACCTTTTGTCCGTTTG	1	24	1
CTCCTTTTCATAAAACTTTTAAGTAAGACT	1	59	1
CGACAAATGTTATAACCTTTCCCGTCTTTT	2	36	0
GATGAAATATAAAAACCTTATTTGAGAAGT	3	25	1
TTAATTAGTTAAATACTTTTTGGCCTAAAT	4	27	0
CTATTCGGATAAATACCTCTTTTAACAAGA	4	164	0
TAAACTTTAAAATTTCCTTTCCCACTTCTT	5	15	1
          **********
MAP Score: 5.5806

Motif 4
AACATTTGAGAGAAAGATATCCGCAACCCTTG	0	59	1
CGAAGTGGTTAAAAGTATTTCCATGCTTTTTG	0	106	0
AAGTTTTATGAAAAGGAGATCATCAAACGGAC	1	45	0
TTCAAAACTGAAAATTAAATTAGAGGTGATAC	1	109	1
ATATTATCACAAAAATAATTTAGGCCAAAAAG	4	10	1
AATTTAGGCCAAAAAGTATTTAACTAATTAAA	4	26	1
CAACTTCCCCAGAATTTAATTCATGGCCTAGA	4	129	1
CTCTTGTTAAAAGAGGTATTTATCCGAATAGA	4	163	1
GAGCTATACAAGGAGGAAATCCAGGAAGAAAT	4	237	1
GAGGAAATCCAGGAAGAAATCCCCGAATACGT	4	249	1
TTGATGTTCAAGAAATAAATTAGTGAAA    	6	6	0
AAGATCGCTTAGGAAGCATTTACTGGTGAAGC	6	75	1
          **** * *****
MAP Score: 4.46393

Motif 5
AACATTTGAGAGAAAGATATCCGCAACCCTTG	0	59	1
CCATGCTTTTTGACCGAAATCAAGACTCAAGG	0	86	0
AAATACTTTTTGGCCTAAATTATTTTTGTGAT	4	15	0
ATTAAAGGCTAGGCTTAGAATAGGGAATTTCA	4	52	1
ATCTAGGCCATGAATTAAATTCTGGGGAAGTT	4	130	0
ATTTAATTCATGGCCTAGATTCTCTTGTTAAA	4	142	1
TTGTTAAAAGAGGTATTTATCCGAATAGAAGC	4	166	1
GAGCTATACAAGGAGGAAATCCAGGAAGAAAT	4	237	1
GAGGAAATCCAGGAAGAAATCCCCGAATACGT	4	249	1
TTGATGTTCAAGAAATAAATTAGTGAAA    	6	6	0
AAGATTTCTTAGACCTTGATCCTCTCAAAGAT	6	41	0
          **** ** ****
MAP Score: 4.34672

Motif 6
GAACATTTGAGAGAAAGATATCCGCAACCCTTGAGTC	0	58	1
TCTTGATTTCGGTCAAAAAGCATGGAAATACTTTTAA	0	93	1
ATCATCAAACGGACAAAAGGTTTTAAATTAACTCCAT	1	22	0
AAAGTTTTATGAAAAGGAGATCATCAAACGGACAAAA	1	41	0
AAATAATTTAGGCCAAAAAGTATTTAACTAATTAAAG	4	22	1
TTGTAGGAATGGCCAAGATGAAAATAATAAGCGTCCA	4	94	1
AAAAGAAGTGGGAAAGGAAATTTTAAAGTTTAAAGTT	5	10	0
ATACATTGATGTTCAAGAAATAAATTAGTGAAA    	6	6	0
GAGGATCAAGGTCTAAGAAATCTTATAAGATCGCTTA	6	49	1
CCCTGAGGATGTTAAAAACGCTATCTAGGTGGAGGTG	7	19	1
          *  ***** **    **
MAP Score: 3.04746

Motif 7
TATTTAATGGTTTAGATGAACATTTGAGAG	0	41	1
AGATGAACATTTGAGAGAAAGATATCCGCA	0	54	1
GTCAAGCTAACTGGGGGGATTGAA      	0	152	1
AAAATTAAATTAGAGGTGATACTC      	1	119	1
TGAAGCGAATTTGGGAGGGATAGAA     	2	78	1
TTAGATAAATTTTGGGGGGAGTGAAAG   	4	283	1
CCCACTTCTTTTTAGGTGATGAA       	5	35	1
CAATGTATCTTTGAGAGGATCAAGGTCTAA	6	35	1
GCTATCTAGGTGGAGGTGATGGC       	7	38	1
          **********
MAP Score: 2.46514

Motif 8
AGATATTGGTAAATGTCAAGCTAACTGGGGGGATTGAA 	0	138	1
CTTTTCATAAAACTTTTAAGTAAGACTAGCGAAAATATT	1	62	1
CGGGAATTCAAAACTGAAAATTAAATTAGAGGTGATACT	1	103	1
        CGAATGTCGAAGTCATTATCGACAAAAAAAG	2	2	1
TCGAAAATCAAAAATTGAAGCGAATTTGGGAGGGATAGA	2	63	1
ACATCGATGAAATATAAAAACCTTATTTGAGAAGTCGAG	3	20	1
AGGAATGGCCAAGATGAAAATAATAAGCGTCCAACTTCC	4	98	1
TTATCCGAATAGAAGCGAAGCCATCAGAGTAGCCATAAG	4	182	1
TGGGAAAGGAAATTTTAAAGTTTAAAGTT          	5	0	0
TGAGAGGATCAAGGTCTAAGAAATCTTATAAGATCGCTT	6	46	1
          **  *  **** *   * *
MAP Score: 1.88654