AlignACE 3.0 10/20/99
AlignACE2 -i HP/HP_fusions005_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944245291
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	HP0282	50	H. pylori predicted coding region HP0282
#1	HP0289	66	toxin-like outer membrane protein
#2	HP0290	47	diaminopimelate decarboxylase (dap decarboxylase) (lysA)
#3	HP0408	165	H. pylori predicted coding region HP0408
#4	HP1279	300	anthranilate isomerase (trpC)
#5	HP1282	222	anthranilate synthase component I (trpE)

Motif 1
ATCCAAGATTAAGGCTTAAACG          	0	0	0
GCTACTATCTAGGAAATGAGAGGGTAGCATTT	1	43	1
ACCTAACCATAAAATTTGAACGAAGCATTATA	2	19	0
GTGTTTTAGAAAGACTTAAGCGCTAAAGACTT	3	35	1
TTAAGCGCTAAAGACTTGAGCGCTAGCCAAGC	3	50	1
ATTATAATATAAAAATTGAGAATTACCCCACG	3	87	0
TATTGAAAACAGAAATTAAACGCATTGATTGG	3	121	0
          GTGAATTGAAAAATAACGGAAT	4	0	1
GAAAAATAACGGAATTTTAGAGTATGACTTGA	4	17	1
ATTTTAGAGTATGACTTGAGCGCTAAAGATTT	4	30	1
TTGCCCCCCTATGATTTGAAAGAATTACAGAT	4	66	1
TGAAAGAATTACAGATTGAAAACGCACAAGAA	4	82	1
CATAAAGCTAAAGATTTAAAAGAGGGTGTGAG	4	210	1
GGGTGTGAGCATGACTTTAGAGCATTTAAAAA	4	233	1
 TTGCGTTATAAGTTTTTAGAGGATAACTTCA	5	9	1
CTAACCACCACCAAATTGAAAGCTTCTTTTCG	5	74	1
          * ** *******
MAP Score: 20.7913

Motif 2
        CGTTTAAGCCTTAATCTTGGATAT	0	2	1
        CTTTTTTGCTATAATGCTTCGTTC	2	2	1
TTTAGAAAGACTTAAGCGCTAAAGACTTGAGC	3	39	1
GCGCTAAAGACTTGAGCGCTAGCCAAGCTGAA	3	54	1
AATAACGGAATTTTAGAGTATGACTTGAGCGC	4	21	1
TAGAGTATGACTTGAGCGCTAAAGATTTTGAT	4	34	1
TGTTTAGATATTTTAGAAAATAAAGGCAAGGA	4	126	1
GTTTGTTGTATTTAAGCCATAAAGCTAAAGAT	4	193	1
GTGAGCATGACTTTAGAGCATTTAAAAACCAA	4	237	1
CGTTATAAGTTTTTAGAGGATAACTTCAGCTT	5	13	1
TAGAGGATAACTTCAGCTTTAGATTGTAAAAG	5	26	1
AAAATTCCTTTTTATGCTTTTACAATCTAAAG	5	42	0
ACGAGTTTATTTTTAGCGTAAAGAAATTG   	5	203	1
          *** **** ***
MAP Score: 9.4417

Motif 3
TTACGCCATTATATCCAAGATTAAGGCTTAAACG  	0	8	0
ATATAATGGCGTAATCATTTTTTAGGAAGT      	0	30	1
ATTTAATCAAATGAGAGAGTTTTTGGCTACTATCTA	1	18	1
ACATACTAGCATGAGGGTGTTTTAGAAAGACTTAAG	3	19	1
GCGTGGGGTAATTCTCAATTTTTATATTATAATACC	3	86	1
TGTTTTCAATATTGACGCTTATAAGGATAAAAG   	3	142	1
GAATTGAAAAATAACGGAATTTTAGAGTATGACTTG	4	12	1
ACTCAAGCGTGTTTAGATATTTTAGAAAATAAAGGC	4	117	1
CCTCTTTTAAATCTTTAGCTTTATGGCTTAAATACA	4	199	0
      TTGCGTTATAAGTTTTTAGAGGATAACTTC	5	4	1
CTTTTCGCACAACCACATTTTTAAGAGAGCAGAATG	5	99	1
AGAGCAGAATGTCTTGGAATTTTTGAAAACGCTCAC	5	124	1
ACGCTCACTCATTAGCGTATTTATTGCCCATTTATC	5	152	1
          **    *  *******
MAP Score: 7.54567

Motif 4
TGGCGTAATCATTTTTTAGGAAGT       	0	36	1
TAATTCTCAATTTTTATATTATAATACCCAA	3	94	1
AAATAACGGAATTTTAGAGTATGACTTGAGC	4	20	1
GTGTTTAGATATTTTAGAAAATAAAGGCAAG	4	125	1
TGTGAGCATGACTTTAGAGCATTTAAAAACC	4	236	1
GCGTTATAAGTTTTTAGAGGATAACTTCAGC	5	12	1
ATGTCTTGGAATTTTTGAAAACGCTCACTCA	5	132	1
ATAAACTCGTATTTTACAAGAAATAGATAAA	5	182	0
TACGAGTTTATTTTTAGCGTAAAGAAATTG 	5	202	1
          ********* *
MAP Score: 6.40842

Motif 5
GCGCTTAAGTCTTTCTAAAACACCCTCATG	3	28	0
CGTGGGGTAATTCTCAATTTTTATATTATA	3	87	1
TTAATTTCTGTTTTCAATATTGACGCTTAT	3	134	1
ATTCCGTTATTTTTCAATTCAC        	4	2	0
ATCTGTAATTCTTTCAAATCATAGGGGGGC	4	68	0
TTCTTGTGCGTTTTCAATCTGTAATTCTTT	4	84	0
CTTGCCTTTATTTTCTAAAATATCTAAACA	4	126	0
GCGCTTTGGTTTTTAAATGCTCTAAAGTCA	4	244	0
TGAAGTTATCCTCTAAAAACTTATAACGCA	5	11	0
TAAAAAGGAATTTTCTAACCACCACCAAAT	5	60	1
CGAAAAGAAGCTTTCAATTTGGTGGTGGTT	5	76	0
TGAGTGAGCGTTTTCAAAAATTCCAAGACA	5	133	0
          **********
MAP Score: 2.9513

Motif 6
ATCTTGGATATAATGGCGTAATCATTTTTTAGGAAGT      	0	23	1
TTTTTTGCTATAATGCTTCGTTCAAATTTTATGGTTAGGTTTT	2	11	1
AGAGTAAACATACTAGCATGAGGGTGTTTTAGAAAGACTTAAG	3	12	1
AGCTGAAGCGTGGGGTAATTCTCAATTTTTATATTATAATACC	3	79	1
     GTGAATTGAAAAATAACGGAATTTTAGAGTATGACTTG	4	5	1
TGCTCTAAAGTCATGCTCACACCCTCTTTTAAATCTTTAGCTT	4	214	0
TATAAGTTTTTAGAGGATAACTTCAGCTTTAGATTGTAAAAGC	5	16	1
GAAAGCTTCTTTTCGCACAACCACATTTTTAAGAGAGCAGAAT	5	91	1
TTCTTTACGCTAAAAATAAACTCGTATTTTACAAGAAATAGAT	5	185	0
          *   *      *  * ***** *
MAP Score: 0.988031

Motif 7
    ACTTCCTAAAAAATGATTACGCCATTATATCCAAGAT	0	23	0
ATGAGGGTGTTTTAGAAAGACTTAAGCGCTAAAGACTTGAG	3	29	1
TTGGGTATTATAATATAAAAATTGAGAATTACCCCACGCTT	3	84	0
     GTGAATTGAAAAATAACGGAATTTTAGAGTATGACT	4	5	1
CCCCCTATGATTTGAAAGAATTACAGATTGAAAACGCACAA	4	70	1
TTATGCGCATTTGCAAAAAATCATAAGGCTAAGCC      	4	275	1
TATAAGTTTTTAGAGGATAACTTCAGCTTTAGATTGTAAAA	5	16	1
GAAAGCTTCTTTTCGCACAACCACATTTTTAAGAGAGCAGA	5	91	1
CTATTTCTTGTAAAATACGAGTTTATTTTTAGCGTAAAGAA	5	187	1
          **  * *  * *  *   ***
MAP Score: 0.567574