AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID061_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943391573
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	nuoN	186	NADH dehydrogenase I chain N
#1	nuoM	163	NADH dehydrogenase I chain M
#2	nuoG	46	NADH dehydrogenase I chain G
#3	nuoC	93	NADH dehydrogenase I chain C, D
#4	nuoA	300	NADH dehydrogenase I chain A
#5	hyfA	213	hydrogenase 4 Fe-S subunit
#6	hycB	124	probable small subunit of hydrogenase-3, iron-sulfur protein (part of formate hydrogenlyase (FHL) complex)

Motif 1
CTCCACAAAACCTGATCGCACTGCTACCGTTGCTGATCGTC	0	26	1
GCATCACAACCACCACCGTCAAGCCGACGATCAGCAACGGT	0	51	0
ATGCTCTCCATTGCGTGGCGACGCAATCATTTCCTCAACGC	0	88	1
GCAATCATTTCCTCAACGCTACGCTCTCGGTTATTGGGCTT	0	110	1
TTATTGGGCTTAACGCGGCGCTGGTTTCGCTCTGGTTTGTT	0	140	1
TTCGCTCTGGTTTGTTGGCCAGGCGGGCGCT          	0	165	1
TCGGATAAGCCGCCTTCGCGGTGCATCCGACACTACCCCCA	1	53	1
ATTCCTAAATCTATTTCGCGAAGCTTACTGCGCCGACAGTC	3	45	1
   TTTTCCATTGCTTCACAACGGACACGATTCAACAACAT	4	7	1
TGCTCCATTCCGTGCTGGCTGCGCTTGCGGCCAGCATACCT	5	16	1
  GCTGAGGCTTTGCCCGTTTTGCAGGCGTTACGCCTGTTT	6	8	1
          *  *  ***   **   ** *
MAP Score: 19.7175

Motif 2
GGCCGCAAGCGCAGCCAGCACGGAATGGAGCAA	5	15	0
GTTGCTGATCGTCGGCTTGACGGTGGTGGTTGT	0	54	1
CGTTGAAAATCCGGTCCTGACGGGACTTTTACA	1	124	1
TCTCGCTTTCCCCTGCGACACGGGTGTCGAATC	5	81	1
GGTCGGATAAGCCGCCTTCGCGGTGCATCCGAC	1	51	1
TACTGCGCCGACAGTCACCACGGACCATTTGCA	3	70	1
CAGGCGTAACGCCTGCAAAACGGGCAAAGCCTC	6	13	0
GCTCTGGTTTGTTGGCCAGGCGGGCGCT     	0	168	1
AGTGAGGTATGCTGGCCGCAAGCGCAGCCAGCA	5	28	0
TAATTATCCTGGAGTCGTCAAGGATCTGGGGTG	4	49	1
AGGAAATGATTGCGTCGCCACGCAATGGAGAGC	0	90	0
GCCAGATTCACTGCTCTTCACGGCAGATGGACG	4	256	0
TGTATTAACTGGATTCTGAACGGTACAAAAATG	5	141	0
CTCTCGGTTATTGGGCTTAACGCGGCGCTGGTT	0	133	1
ATTTTCGACACTCATCGACACGCCCATCCCCAA	6	47	0
  TTTTCCATTGCTTCACAACGGACACGATTCA	4	8	1
          ** ***  *****
MAP Score: 15.1038

Motif 3
GTGACTGTCGGCGCAGTAAGCTTCGCGAAATAGATT	3	52	0
TGGGCTTAACGCGGCGCTGGTTTCGCTCTGGTTTGT	0	144	1
TAGCGTTGAGGAAATGATTGCGTCGCCACGCAATGG	0	95	0
GCCGTGAAGAGCAGTGAATCTGGCGCTACTTTTGAT	4	265	1
AAACCTGATCGCACTGCTACCGTTGCTGATCGTCGG	0	33	1
ACGTAGGTCGGATAAGCCGCCTTCGCGGTGCATCCG	1	46	1
    GCTGAGGCTTTGCCCGTTTTGCAGGCGTTACG	6	6	1
TTTGCTCCATTCCGTGCTGGCTGCGCTTGCGGCCAG	5	14	1
AAAAATGGATTCGACACCCGTGTCGCAGGGGAAAGC	5	85	0
TTAAGCCCAATAACCGAGAGCGTAGCGTTGAGGAAA	0	117	0
AGATGTTGTTGAATCGTGTCCGTTGTGAAGCAATGG	4	14	0
          **   *   *******
MAP Score: 12.5021

Motif 4
TAGCGTTGAGGAAATGATTGCGTCGCCACGCAATGG	0	95	0
AAACCTGATCGCACTGCTACCGTTGCTGATCGTCGG	0	33	1
GCCGTGAAGAGCAGTGAATCTGGCGCTACTTTTGAT	4	265	1
ACGTAGGTCGGATAAGCCGCCTTCGCGGTGCATCCG	1	46	1
GTGACTGTCGGCGCAGTAAGCTTCGCGAAATAGATT	3	52	0
CTCGGTTATTGGGCTTAACGCGGCGCTGGTTTCGCT	0	135	1
    GCTGAGGCTTTGCCCGTTTTGCAGGCGTTACG	6	6	1
TCCTGGAGTCGTCAAGGATCTGGGGTGAAAGGGCAT	4	55	1
AGATGTTGTTGAATCGTGTCCGTTGTGAAGCAATGG	4	14	0
CGGCTTGACGGTGGTGGTTGTGATGCTCTCCATTGC	0	66	1
CCAGTCCGAAGAGAATTTTCTGTCGTGAGAATTCGT	1	91	1
         TGCAAATGGTCCGTGGTGACTGTCGGC	3	76	0
CGCCTGTTTGGGGATGGGCGTGTCGATGAGTGTCGA	6	40	1
GTAAACTAATGTGAAGAAACTTTTGTTAAAGTTGAC	4	116	1
TAAGGATTGTGGGATTGCCCCTGGGCATATAAGAAC	1	12	1
TTCGGACTGGGGGTAGTGTCGGATGCACCGCGAAGG	1	65	0
TCTTGATCACGAGAAGTGAGGTATGCTGGCCGCAAG	5	39	0
          *   **   *******
MAP Score: 11.1448

Motif 5
GCACTGCTACCGTTGCTGATCGTCGGCTTGACGG	0	43	1
GTCGGCTTGACGGTGGTGGTTGTGATGCTCTCCA	0	64	1
CTCTCGGTTATTGGGCTTAACGCGGCGCTGGTTT	0	133	1
TGGTTTCGCTCTGGTTTGTTGGCCAGGCGGGCGC	0	161	1
TCTCTTCGGACTGGGGGTAGTGTCGGATGCACCG	1	71	0
CGTTGAAAATCCGGTCCTGACGGGACTTTTACAA	1	124	1
AGAAAAATCCCTTTGCCGACAGGCGCAAA     	3	5	0
TGCAAATGGTCCGTGGTGACTGTCGGCGCAGTAA	3	69	0
CGTCAAGGATCTGGGGTGAAAGGGCATTAAATGC	4	64	1
TTGCTCCATTCCGTGCTGGCTGCGCTTGCGGCCA	5	15	1
GATTCGACACCCGTGTCGCAGGGGAAAGCGAGAA	5	80	0
GAGGCTTTGCCCGTTTTGCAGGCGTTACGCCTGT	6	13	1
TACGCCTGTTTGGGGATGGGCGTGTCGATGAGTG	6	38	1
          ***** **   ***
MAP Score: 7.45302

Motif 6
AAAACCTGATCGCACTGCTACCGTTGCTGATCGTCGG	0	32	1
TCCATTGCGTGGCGACGCAATCATTTCCTCAACGCTA	0	94	1
CAATCATTTCCTCAACGCTACGCTCTCGGTTATTGGG	0	111	1
TTGGGCTTAACGCGGCGCTGGTTTCGCTCTGGTTTGT	0	143	1
AAGCCGCCTTCGCGGTGCATCCGACACTACCCCCAGT	1	59	1
AAATCTATTTCGCGAAGCTTACTGCGCCGACAGTCAC	3	51	1
CTTTGCTCCATTCCGTGCTGGCTGCGCTTGCGGCCAG	5	13	1
GCTGCGCTTGCGGCCAGCATACCTCACTTCTCGTGAT	5	33	1
AGGCTTTGCCCGTTTTGCAGGCGTTACGCCTGTTTGG	6	14	1
          ***   ***  * ** *
MAP Score: 7.43218

Motif 7
AAACCTGATCGCACTGCTACCGTTGCTGATCGTCGGCT	0	33	1
GCAATGGAGAGCATCACAACCACCACCGTCAAGCCGAC	0	64	0
CCATTGCGTGGCGACGCAATCATTTCCTCAACGCTACG	0	95	1
TTTCCTCAACGCTACGCTCTCGGTTATTGGGCTTAACG	0	117	1
ACAAACCAGAGCGAAACCAGCGCCGCGTTAAGCCCAAT	0	142	0
ACGTAGGTCGGATAAGCCGCCTTCGCGGTGCATCCGAC	1	46	1
AATCTATTTCGCGAAGCTTACTGCGCCGACAGTCACCA	3	52	1
TTTGCTCCATTCCGTGCTGGCTGCGCTTGCGGCCAGCA	5	14	1
CTTGCGGCCAGCATACCTCACTTCTCGTGATCAAGATC	5	39	1
AAAAATGGATTCGACACCCGTGTCGCAGGGGAAAGCGA	5	83	0
    GCTGAGGCTTTGCCCGTTTTGCAGGCGTTACGCC	6	6	1
CGTTTTGCAGGCGTTACGCCTGTTTGGGGATGGGCGTG	6	24	1
          **   **   * **** *
MAP Score: 5.523

Motif 8
TGTGGAGTTATTGTCATGGCGAT         	0	1	0
TTGCTGATCGTCGGCTTGACGGTGGTGGTTGT	0	55	1
TCTCGGTTATTGGGCTTAACGCGGCGCTGGTT	0	134	1
CTCTGGTTTGTTGGCCAGGCGGGCGCT     	0	169	1
GTCGGATGCACCGCGAAGGCGGCTTATCCGAC	1	52	0
GTTGAAAATCCGGTCCTGACGGGACTTTTACA	1	125	1
        TTTGCGCCTGTCGGCAAAGGGATT	3	2	1
TGCAAATGGTCCGTGGTGACTGTCGGCGCAGT	3	71	0
CGTCAAGGATCTGGGGTGAAAGGGCATTAAAT	4	64	1
TGGCGTCCATCTGCCGTGAAGAGCAGTGAATC	4	253	1
TTGCTCCATTCCGTGCTGGCTGCGCTTGCGGC	5	15	1
TCCCCTGCGACACGGGTGTCGAATCCATTTTT	5	89	1
GCCCGTTTTGCAGGCGTTACGCCTGTTTGGGG	6	21	1
TGTTTGGGGATGGGCGTGTCGATGAGTGTCGA	6	44	1
          * *** ******
MAP Score: 4.70236

Motif 9
ACAACCACCACCGTCAAGCCGACGATCAGCAACG	0	53	0
CGCAATCATTTCCTCAACGCTACGCTCTCGGTTA	0	109	1
TCGGTTATTGGGCTTAACGCGGCGCTGGTTTCGC	0	136	1
TCTGGTTTGTTGGCCAGGCGGGCGCT        	0	170	1
GTCGGATAAGCCGCCTTCGCGGTGCATCCGACAC	1	52	1
GTTGAAAATCCGGTCCTGACGGGACTTTTACAAG	1	125	1
        TTTGCGCCTGTCGGCAAAGGGATTTT	3	2	1
CCAGATTCACTGCTCTTCACGGCAGATGGACGCC	4	254	0
TTGCTCCATTCCGTGCTGGCTGCGCTTGCGGCCA	5	15	1
ATCACATTCTCGCTTTCCCCTGCGACACGGGTGT	5	74	1
GAGGCTTTGCCCGTTTTGCAGGCGTTACGCCTGT	6	13	1
TGTTTGGGGATGGGCGTGTCGATGAGTGTCGAAA	6	44	1
          *** *  * *****
MAP Score: 2.33245

Motif 10
CGTTGCTGATCGTCGGCTTGACGGTGGTGGTTGTGA	0	53	1
AGAAAATTCTCTTCGGACTGGGGGTAGTGTCGGATG	1	76	0
TCGTTGAAAATCCGGTCCTGACGGGACTTTTACAAG	1	123	1
CGATTAACGCTCAGTCTCTGACTGAGAAAACTGGAA	2	18	1
          TTTGCGCCTGTCGGCAAAGGGATTTT	3	0	1
CAAATGGTCCGTGGTGACTGTCGGCGCAGTAAGCTT	3	65	0
CTGGAGTCGTCAAGGATCTGGGGTGAAAGGGCATTA	4	57	1
ATCGATGTGGCGTCCATCTGCCGTGAAGAGCAGTGA	4	246	1
CTTTGCTCCATTCCGTGCTGGCTGCGCTTGCGGCCA	5	13	1
CTGAGGCTTTGCCCGTTTTGCAGGCGTTACGCCTGT	6	11	1
GCAGGCGTTACGCCTGTTTGGGGATGGGCGTGTCGA	6	30	1
          *  **  *** *** *
MAP Score: 0.400981