AlignACE 3.0 10/20/99
AlignACE2 -i HP/HP_fusions006_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944245335
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	HP0667	300	H. pylori predicted coding region HP0667
#1	HP1354	24	putative adenine specific DNA methyltransferase
#2	HP1360	28	4-hydroxybenzoate octaprenyltransferase (ubiA)
#3	HP1361	56	competence locus E (comE3)
#4	HP1365	83	response regulator
#5	HP1368	300	type IIS restriction enzyme M2 protein (mod)

Motif 1
TAAGAAGTTCAAACGCCCCCTGAAAAGTTT	3	16	0
CATTTTTTTAAAATACCCCCATTTCATTGT	5	228	1
GTTTGCATCGTAATCCCCCCAAA       	0	3	0
ATTAGCGCTACAATACCCCC          	4	73	1
TTAAGCGCTACAATACCCCCATGCAAAAAA	5	111	1
GGTTATAAAAAAACACTCCCTTAAAAAAGA	4	25	0
        GTTAATAACCCCTTTTTAAAGT	1	12	0
TAGACGACCCTAACACTCCGCCATTTTTGC	0	161	1
GTTTTCATTATAACGCTCCTTAAAAAACAT	5	54	1
TCAAACTCCTTAACGCTCTCGCTTAAAAGG	5	166	0
CTTTTAAAGAAAATCCCGCCTTTTGTGTTT	0	29	0
GGCTTTGTTATAATACTTCCTATGTTTTTT	5	75	0
TTTGAACTTCTTACGACCCCCAAAGAATAC	3	33	1
TACAGAGCTTTAACGCCACTATAAGGAATG	0	276	1
          **********
MAP Score: 20.3716

Motif 2
TCTTTAGCCCTAAGAAGCCCCACTTTTAAAG	0	50	0
CCATATGCAATTAAACAACGCTTTAAAGTCT	0	129	1
TTTAAAGTCTTTAGACGACCCTAACACTCCG	0	150	1
TAGACGACCCTAACACTCCGCCATTTTTGCA	0	161	1
CGCTAAAGCCTTAAAAAGCGCTGAATAAAAA	0	207	1
AAAGCGCTGAATAAAAAGCCTTTTTAACCCC	0	221	1
         GTTAATAACCCCTTTTTAAAGT	1	12	0
CGTAAGAAGTTCAAACGCCCCCTGAAAAGTT	3	17	0
TTTGAACTTCTTACGACCCCCAAAGAATACC	3	33	1
TACGACCCCCAAAGAATACCTG         	3	44	1
CTCCCTTAAAAAAGACACCGCTTTATTTTA 	4	9	0
GGTTATAAAAAAACACTCCCTTAAAAAAGAC	4	24	0
GCAATTAGCGCTACAATACCCCC        	4	70	1
TTATGAAGTTTTAGAAAACCTTTTCATAG  	5	8	0
GGAAGTATTATAACAAAGCCCGCTCATTAAG	5	85	1
TCATTAAGCGCTACAATACCCCCATGCAAAA	5	108	1
ACTCATTTTTTTAAAATACCCCCATTTCATT	5	225	1
AAATTCTTTCATGCAAAACCCATTGAAGTTT	5	259	1
          ****** ****
MAP Score: 16.5824

Motif 3
  AGACTTTAAAAAGGGGTTATTAAC       	1	8	1
CCCATGCAAAAAAAGATTTTTTTATTAGAAGAC	5	128	1
CCTTTATACTAAAAGCGGTTATAAAAAAACACT	4	38	0
     CTATGAAAAGGTTTTCTAAAACTTCATA	5	5	1
GCGCTGAATAAAAAGCCTTTTTAACCCCATTCT	0	224	1
GATTTTCTTTAAAAGTGGGGCTTCTTAGGGCTA	0	44	1
ATGCAAACACAAAAGGCGGGATTTTCTTTAAAA	0	25	1
    TAAAATAAAGCGGTGTCTTTTTTAAGGGA	4	6	1
TAGTGGCGTTAAAGCTCTGTATTATATAAAAAG	0	264	0
TAAAGACTTTAAAGCGTTGTTTAATTGCATATG	0	130	0
TTTTACAATGAAATGGGGGTATTTTAAAAAAAT	5	229	0
CGCCCCCTGAAAAGTTTTGTCTT          	3	0	0
TGTCTTTTTTAAGGGAGTGTTTTTTTATAACCG	4	23	1
GTATTATATAAAAAGATGTTGGAGAATGGGGTT	0	246	0
          AAAAGTCATTTTATTAGGGATCA	2	0	1
AAAGCCTTAAAAAGCGCTGAATAAAAAGCCTTT	0	211	1
          *****  *** **
MAP Score: 15.3771

Motif 4
TGTTTGCATCGTAATCCCCCCAAA       	0	3	0
ACTTTTAAAGAAAATCCCGCCTTTTGTGTTT	0	29	0
TTTAGCCCTAAGAAGCCCCACTTTTAAAGAA	0	48	0
ATTGCATATGGCATGCCCCGCATTCAGCGCT	0	109	0
TAAGAAGTTCAAACGCCCCCTGAAAAGTTTT	3	15	0
TTTGAACTTCTTACGACCCCCAAAGAATACC	3	33	1
AATTAGCGCTACAATACCCCC          	4	72	1
AAGTATTATAACAAAGCCCGCTCATTAAGCG	5	87	1
ATTAAGCGCTACAATACCCCCATGCAAAAAA	5	110	1
TCATTTTTTTAAAATACCCCCATTTCATTGT	5	227	1
          * *********
MAP Score: 14.8771

Motif 5
GACTGACTCATTTTTTTAAAATACCCCCAT	5	220	1
TATTTTTACCTTTTATTAAACTTCAATGGG	5	277	0
AAAGCGGTGTCTTTTTTAAGGGAGTGTTTT	4	16	1
  AAAAGTCATTTTATTAGGGATCAAATCA	2	8	1
ACTTCCTATGTTTTTTAAGGAGCGTTATAA	5	61	0
AAAAAGATTTTTTTATTAGAAGACGATTAC	5	137	1
TTAATAACCCCTTTTTAAAGTCT       	1	3	0
TTATTCAGCGCTTTTTAAGGCTTTAGCGAT	0	205	0
AAGGCGGGATTTTCTTTAAAAGTGGGGCTT	0	37	1
TATGAAAAGGTTTTCTAAAACTTCATAAAA	5	11	1
TAAAAAGGCTTTTTATTCAGCGCTTTTTAA	0	217	0
TAAGGGAGTGTTTTTTTATAACCGCTTTTA	4	32	1
TTTTCTAAAACTTCATAAAATTGCGCTTCG	5	21	1
TCCAACATCTTTTTATATAATACAGAGCTT	0	256	1
CTTCGTTCGTTTTCATTATAACGCTCCTTA	5	46	1
GGCGTTTGAACTTCTTACGACCCCCAAAGA	3	29	1
CGCTAATTGCCTTTATACTAAAAGCGGTTA	4	50	0
AAAGACACCGCTTTATTTTA          	4	0	0
          **********
MAP Score: 13.9415