AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID021_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943391114
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	cydA	300	cytochrome d terminal oxidase, polypeptide subunit I
#1	hyaA	300	hydrogenase-1 small subunit
#2	appC	133	probable third cytochrome oxidase, subunit I

Motif 1
ATTGGCTGAAAGGCGGTAATTTAGCTATAA	0	31	1
TTGCATTTTTCGACGGTGATCAATTTATAG	0	55	0
CACACAAAAACGGCGTAAAGAAAGGTTGCA	0	171	0
CGGAGTCTTCATGCGATGAGCAAGGAGTC 	0	281	1
CCCCACCGCCCGGCCAAAAGAAAAATAGGT	1	51	1
CGTCGCTTGCCGACCATAAGCGCCCGGTGT	1	246	1
CGGTGTCGCAAGGAGGAGAGACGTGCGAT 	1	281	1
        AAAGACGGTAAGTATCGCTTTC	2	2	1
GATATTCATAAGACTGAAAGCGATACTTAC	2	17	0
GCACTCCTGTAGGCGAAGAGAGAAAAATAA	2	111	0
          **********
MAP Score: 8.13764

Motif 2
AATAAACAGGTTTTTGTTGAAGCAAATTTGCAT	0	79	0
TTCAAACAAATTTCTATTGGGGCATGCGTGTGA	0	225	1
AATGGACCTATTTTTCTTTTGGCCGGGCGGTGG	1	53	0
ACTGTGTGGATTTATCTTTTAGCGATAAAAATG	1	82	0
ACACAGTTTGTATTGTTTTGTGCAAAAGTTTCA	1	108	1
AAGGATGAGCTTTCGTTTTCAGCATCTCACGTG	1	186	1
AGACGGTAAGTATCGCTTTCAGTCTTATGAATA	2	12	1
TCGGGTTATTTTTCTCTCTTCGCCTACAGGAGT	2	106	1
          ***** ***  **
MAP Score: 7.30807

Motif 3
AAATTGGCTGAAAGGCGGTAATTTAGCTATA	0	29	1
ATAAATTGATCACCGTCGAAAAATGCAAATT	0	57	1
GAAAGGTTGCAAACATGTTAATAAAAACTCA	0	151	0
TGCACACAAAAACGGCGTAAAGAAAGGTTGC	0	172	0
GACCCTTTCTAACGGGGTTCACTCTCGGAGT	0	256	1
GCCGGTTGCTAAACGAGTAAAAGAGAAGGAA	1	13	0
CTCGTTTAGCAACCGGCTAAACATCCCCACC	1	27	1
GCCGGTGTCGCAAGGAGGAGAGACGTGCGAT	1	279	1
          AAAGACGGTAAGTATCGCTTT	2	0	1
GTTTCAGGATAAAGAGGGAGATCTACCATTA	2	75	1
          ***** *****
MAP Score: 4.55402

Motif 4
AATTTCTATTGGGGCATGCGTGTGACCCTT	0	233	1
ATACTTTCTGGCGACGTGCGCCAGTGCAGA	1	157	1
TGGTCGGCAAGCGACGTCCCTGTAGCAAGG	1	232	0
GCAAGGAGGAGAGACGTGCGAT        	1	288	1
TCTTCGCCTACAGGAGTGCGC         	2	122	1
          **********
MAP Score: 2.92407

Motif 5
TTGAAGCAAATTTGCATTTTTCGACGGTGAT	0	65	0
GTGGGATCAATTTGAGTTTTTATTAACATGT	0	139	1
ATTCCTTCTCTTTTACTCGTTTAGCAACCGG	1	12	1
AATGGACCTATTTTTCTTTTGGCCGGGCGGT	1	55	0
AATAGGTCCATTTTTATCGCTAAAAGATAAA	1	74	1
ATCCACACAGTTTGTATTGTTTTGTGCAAAA	1	104	1
GAAGCGATGGTTTGCCTTGCTACAGGGACGT	1	218	1
TATCGGGTTATTTTTCTCTCTTCGCCTACAG	2	104	1
          **** ******
MAP Score: 2.71673

Motif 6
AATTTCTATTGGGGCATGCGTGTGACCCTT	0	233	1
TCTTTTGGCCGGGCGGTGGGGATGTTTAGC	1	42	0
ATACTTTCTGGCGACGTGCGCCAGTGCAGA	1	157	1
CCTTGCTACAGGGACGTCGCTTGCCGACCA	1	232	1
CGACACCGGCAGGACACCGGGCGCTTATGG	1	259	0
TCTCCTCCTTGCGACACCGGCAGGACACCG	1	270	0
GCAAGGAGGAGAGACGTGCGAT        	1	288	1
          **********
MAP Score: 2.43887

Motif 7
TACTCGTTTAGCAACCGGCTAAACATCCCC	1	25	1
AACATCCCCACCGCCCGGCCAAAAGAAAAA	1	46	1
ATACTTTCTGGCGACGTGCGCCAGTGCAGA	1	157	1
TGGTCGGCAAGCGACGTCCCTGTAGCAAGG	1	232	0
CCGACCATAAGCGCCCGGTGTCCTGCCGGT	1	255	1
CGCCCGGTGTCCTGCCGGTGTCGCAAGGAG	1	266	1
GCACGTCTCTCCTCCTTGCGACACCGGCAG	1	277	0
GCAAGGAGGAGAGACGTGCGAT        	1	288	1
TATGAATATCGCAATCGGCGAATACCTCTG	2	37	1
          **********
MAP Score: 2.30305

Motif 8
ATATACGTGGGATCAATTTGAGTTTTTATTAACAT	0	133	1
CCGTTTTTGTGTGCATTCACATGGTATGATGAAAG	0	188	1
AAATTTGTTTGAACACTTTCATCATACCATGTGAA	0	203	0
TTCTAACGGGGTTCACTCTCGGAGTCTTCATGCGA	0	262	1
AAGGATGAGCTTTCGTTTTCAGCATCTCACGTGAA	1	186	1
AGACGGTAAGTATCGCTTTCAGTCTTATGAATATC	2	12	1
ACCTCTGGTCGTAGAGTTTCAGGATAAAGAGGGAG	2	60	1
GAGGGAGATCTACCATTATCGGGTTATTTTTCTCT	2	88	1
          ** ** * ****  *
MAP Score: 1.56159