AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID077_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943391954
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	hyaA	300	hydrogenase-1 small subunit
#1	b2997	188	putative hydrogenase subunit
#2	b2998	118	orf, hypothetical protein
#3	b3000	205	orf, hypothetical protein

Motif 1
TTTAGCCGGTTGCTAAACGAGTAAAAGAGAAGGAATTC	0	10	0
TTTAGCAACCGGCTAAACATCCCCACCGCCCGGCCAAA	0	31	1
CCCACCGCCCGGCCAAAAGAAAAATAGGTCCATTTTTA	0	52	1
CCATTTTTATCGCTAAAAGATAAATCCACACAGTTTGT	0	81	1
TATTGTTTTGTGCAAAAGTTTCACTACGCTTTATTAAC	0	118	1
TGCGGCGGGGCGCTAAAACGAAGGGAAGAAGCATTAGT	1	45	0
TTGCCTCAATCGCAAAATCAATAATGCGATCGATGCGC	1	124	0
TTGCGATTGAGGCAAAATATATGCCAGGTCTTCGCAAC	1	147	1
AAATAGCGTGCGCAAAAGTCGTTCTTTGCCTAAAATAT	2	53	1
GCTGGCGAATCGCTAAACTAGAAACATTGTTTCGAAAT	3	32	0
CGAAAAACTGGGCAAAAATACGTGCTTATGCTTTGCTT	3	100	1
CGCGTTTAACCGCCAAAGATTTCCCACAAGAGTTGCTG	3	170	1
          *******      *  **
MAP Score: 6.3386

Motif 2
TGGTGTTTTTTTAAGCAAAGCATAAGCACGTATTTT	3	114	0
TATGACAATATATAGCGAATGAGGTGAACG      	2	98	1
GGATTTATCTTTTAGCGATAAAAATGGACCTATTTT	0	72	0
GCGACGTCCCTGTAGCAAGGCAAACCATCGCTTCAC	0	216	0
TAGCGATATTTTAGGCAAAGAACGACTTTTGCGCAC	2	60	0
AACAATACTTTCTGGCGACGTGCGCCAGTGCAGAAG	0	153	1
ATGTTTCTAGTTTAGCGATTCGCCAGCGCGTATCCC	3	43	1
ATTTTGCGATTGAGGCAAAATATATGCCAGGTCTTC	1	144	1
TGTAATTAATTAAAGCAAGATAATACGTATGTTTGA	1	10	0
GTGGGAAATCTTTGGCGGTTAAACGCGGCATCGTTG	3	161	0
     AGTAATCCAGCAACTCTTGTGGGAAATCTTT	3	184	0
GTATTGTTAATAAAGCGTAGTGAAACTTTTGCACAA	0	125	0
AGCTTTCGTTTTCAGCATCTCACGTGAAGCGATGGT	0	193	1
          * ****** * *   *
MAP Score: 5.70138

Motif 3
CCGGGCGGTGGGGATGTTTAGCCGGTTGCTAAAC	0	30	0
CTCACGTGAAGCGATGGTTTGCCTTGCTACAGGG	0	211	1
TTGCTACAGGGACGTCGCTTGCCGACCATAAGCG	0	234	1
CCATAAGCGCCCGGTGTCCTGCCGGTGTCGCAAG	0	259	1
GAAGACCTGGCATATATTTTGCCTCAATCGCAAA	1	146	0
GTGCGCAAAAGTCGTTCTTTGCCTAAAATATCGC	2	60	1
CAGCGCGTATCCCGTAGTCTGGCTCACAGAGTGA	3	66	1
AAAATACGTGCTTATGCTTTGCTTAAAAAAACAC	3	114	1
AACTCTTGTGGGAAATCTTTGGCGGTTAAACGCG	3	170	0
          *  **  *******
MAP Score: 5.17247

Motif 4
TGTTAATAAAGCGTAGTGAAACTTTTGCACAAAAC	0	122	0
ATACTTTCTGGCGACGTGCGCCAGTGCAGAAGGAT	0	157	1
AGCATCTCACGTGAAGCGATGGTTTGCCTTGCTAC	0	206	1
TGGTCGGCAAGCGACGTCCCTGTAGCAAGGCAAAC	0	227	0
TAAGCGCCCGGTGTCCTGCCGGTGTCGCAAGGAGG	0	262	1
CTTCGTTTTAGCGCCCCGCCGCAGTATCATGATAT	1	60	1
GTGGTAAATGGCGCATCGATCGCATTATTGATTTT	1	114	1
TTATTCCGTTGCGAAGACCTGGCATATATTTTGCC	1	157	0
ATACGCGCTGGCGAATCGCTAAACTAGAAACATTG	3	41	0
AACACCAACTGAGGAGTGCAACGATGCCGCGTTTA	3	143	1
          *** *****  *  *
MAP Score: 4.08763

Motif 5
CTCTTTTACTCGTTTAGCAACCGGCTAAACATC	0	19	1
TAAACATCCCCACCGCCCGGCCAAAAGAAAAAT	0	44	1
ACAGGGACGTCGCTTGCCGACCATAAGCGCCCG	0	239	1
CATAAGCGCCCGGTGTCCTGCCGGTGTCGCAAG	0	260	1
CCCTTCGTTTTAGCGCCCCGCCGCAGTATCATG	1	58	1
TATTCCGTTGCGAAGACCTGGCATATATTTTGC	1	158	0
TCTAGTTTAGCGATTCGCCAGCGCGTATCCCGT	3	48	1
AACGATGCCGCGTTTAACCGCCAAAGATTTCCC	3	162	1
          ** ** ** ****
MAP Score: 3.42944

Motif 6
CGGCCAAAAGAAAAATAGGTCCATTTTTATCG	0	61	1
TTTATCGCTAAAAGATAAATCCACACAGTTTG	0	86	1
ACGCTTTATTAACAATACTTTCTGGCGACGTG	0	143	1
ACCATCGCTTCACGTGAGATGCTGAAAACGAA	0	197	0
TTATGGTCGGCAAGCGACGTCCCTGTAGCAAG	0	233	0
GCGATTGAGGCAAAATATATGCCAGGTCTTCG	1	149	1
ATAGCGTGCGCAAAAGTCGTTCTTTGCCTAAA	2	55	1
AAAACTGGGCAAAAATACGTGCTTATGCTTTG	3	103	1
CGTTTAACCGCCAAAGATTTCCCACAAGAGTT	3	172	1
AAAGATTTCCCACAAGAGTTGCTGGATTACT 	3	184	1
          *******  ***
MAP Score: 2.83979

Motif 7
TAGTGAAACTTTTGCACAAAACAATACAAACTGTGTGGA	0	105	0
AGGGACGTCGCTTGCCGACCATAAGCGCCCGGTGTCCTG	0	241	1
TTGCGAAGACCTGGCATATATTTTGCCTCAATCGCAAAA	1	145	0
AAAGTCGTTCTTTGCCTAAAATATCGCTATATATGACAA	2	67	1
GGGATACGCGCTGGCGAATCGCTAAACTAGAAACATTGT	3	40	0
ATCCCGTAGTCTGGCTCACAGAGTGACGAAAAACTGGGC	3	74	1
GTGCTTATGCTTTGCTTAAAAAAACACCAACTGAGGAGT	3	121	1
          *****  * *   *  * *
MAP Score: 0.112834