AlignACE 3.0 10/20/99
AlignACE2 -i AA/AA_operons010_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944235255
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	atpB	49	ATP synthase F0 subunit a
#1	frdB2_topA	39	frdB2: fumarate reductase iron-sulfur subunit, topA: topoisomerase I
#2	mbhS1	300	hydrogenase small subunit
#3	atpA	63	ATP synthase F1 alpha subunit
#4	thdF	145	thiophene and furan oxidation protein
#5	topG2	130	reverse gyrase
#6	topG1	276	reverse gyrase
#7	aq_1187	48	putative protein
#8	aq_1191	74	hypothetical protein
#9	aq_1596	236	putative protein
#10	atpG1	70	ATP synthase F1 gamma subunit

Motif 1
    TTCCCTTACCTCTTTTGCAATTGGCTCAGA	0	29	0
AGGGTTCGACTCCCTCCACCCCCACCACCCAACC	4	10	0
ATTTTAAGTCCCCCGCGTCTGCCAATTCCGCCAC	4	65	1
CGTCTGCCAATTCCGCCACACCCCCTAACTAAAG	4	80	1
TATTAAGATATACCTCTTTCCCGAAGATGACAAG	5	52	1
   ACATACCTTCCTCTTTTTCCATTTCTTCTAT	6	7	1
TCTTGAGGGCTTCCTCTTCATCCAGCTTTTGTAT	6	64	1
          TACCTCTTCCTCCAGAAAAGAGTT	8	0	1
      CCTTTACCTCCTTTGCGAAGGTTTAAAT	10	4	1
          * **** **  ***
MAP Score: 16.6433

Motif 2
       TTCCCTTACCTCTTTTGCAATTGGC	0	34	0
TCCAGAGTGTCTTTTTCTTCGAACTCCGCAGG	2	108	0
ACCACGTCGCCTTTTCCGTTCAGTTTAGCCTG	2	180	0
CGACGTGGTTATTTACCTTCCTTAAGGAATTT	2	203	1
         ACTCTACCTCCTAACCTTCTTTA	3	50	0
TAAGTATAATATATTTCTTTAGTTAGGGGGTG	4	98	0
GATTATTAAGATATACCTCTTTCCCGAAGATG	5	49	1
          ACATACCTTCCTCTTTTTCCAT	6	0	1
TCCTCTTTTTCCATTTCTTCTATTATTTCTTC	6	18	1
ATTTCTTCTATTATTTCTTCGAAAAGCTCAAG	6	30	1
TGAGGGCTTCCTCTTCATCCAGCTTTTGTATG	6	67	1
TTCGAGGGAAATTTTCCTTTTGACTCCGAGGG	6	155	1
TCCACAAGGGCTGTTCCGTCCTCGTAAACTTC	6	189	1
ATGTGCTTGGCTATACCTTCTAAAGTTGTGGA	6	219	0
TTTAATAATTATATTCCTTCGGTGAATGG   	6	257	1
       TACCTCTTCCTCCAGAAAAGAGTTT	8	3	1
TTCTGAGTATCTCTTCCCTTCGCTTTTGTTCC	9	49	1
CCCTTCGCTTTTGTTCCTTTCTGTACTTGTAG	9	64	1
TCCTCGGAGTCCTTATCTTTATGGCGTACGCT	9	98	0
         CCTTTACCTCCTTTGCGAAGGTT	10	1	1
          ** ******* *
MAP Score: 13.9659

Motif 3
GACGTGGTTATTTACCTTCCTTAAGGAATTTTTAT	2	204	1
TGTGCTACAATAAACCTTTAAAGAAGGTTAGGAGG	3	32	1
AAGTATAATATATTTCTTTAGTTAGGGGGTGTGGC	4	94	0
TATTAAGATATACCTCTTTCCCGAAGATGACAAGT	5	52	1
TTTCTTCTATTATTTCTTCGAAAAGCTCAAGACTC	6	31	1
TCTTGAGGGCTTCCTCTTCATCCAGCTTTTGTATG	6	64	1
TTAATAATTATATTCCTTCGGTGAATGG       	6	258	1
          TACCTCTTCCTCCAGAAAAGAGTTT	8	0	1
AGTAATTAGTTTATTCTTCCCAAAGGTCCTCGTAA	9	10	1
ACCTTCTGAGTATCTCTTCCCTTCGCTTTTGTTCC	9	46	1
TAGTATAATTTAAACCTTCGCAAAGGAGGTAAAGG	10	10	0
GTTTAAATTATACTACTTCCTTTAGACATTAGTTT	10	30	1
          **  ******   **
MAP Score: 13.9492

Motif 4
TGTACCCTGCGGAGTTCGAAGAAAAAGACAC	2	103	1
AAGAAGGTTAGGAGGTAGAGT          	3	52	1
GTTGGGTGGTGGGGGTGGAGGGAGTCGAACC	4	11	1
TACAAAAGCTGGATGAAGAGGAAGCCCTCAA	6	66	0
GGTTCTGGCATGAGTTCGAGGGAAATTTTCC	6	141	1
ATTTTCCTTTTGACTCCGAGGGTATCCACAA	6	165	1
ACTCTTTTCTGGAGGAAGAGGTA        	8	2	0
TACTCAGAAGGTATTACGAGGACCTTTGGGA	9	27	0
ATAAAGATAAGGACTCCGAGGAGTATGAAGG	9	108	1
CCTTCGCAAAGGAGGTAAAGG          	10	0	0
          ***** *****
MAP Score: 12.7395

Motif 5
          TTCCCTTACCTCTTTTGCAATTGG	0	35	0
CAAAATTTTATAGCTTTAGAATTTATTATCCAGA	1	12	0
CGAAAATCTGTACCCTGCGGAGTTCGAAGAAAAA	2	95	1
GTTATTTACCTTCCTTAAGGAATTTTTATGATTT	2	210	1
AAACTAAGTTTAGCTTACGATTATTAAGATATAC	5	31	1
ATCAGAGTAATTGCCTGAGAAGATTTCCCCGCCT	5	87	1
       ACATACCTTCCTCTTTTTCCATTTCTT	6	3	1
AATAATTATATTCCTTCGGTGAATGG        	6	260	1
AATATAAAAATTCCTTAATAATTTTACAAGGGTC	8	44	1
GTCCTCGTAATACCTTCTGAGTATCTCTTCCCTT	9	35	1
TGAGTATCTCTTCCCTTCGCTTTTGTTCCTTTCT	9	52	1
TTCGCTTTTGTTCCTTTCTGTACTTGTAGTAAGC	9	67	1
TAGTGGGAATTACCTTAATTCCCTTCATACTCCT	9	126	0
TTAGCAGGTTTTGCATTCGGATTTCTCTTAGCTG	9	169	0
ATTATACTACTTCCTTTAGACATTAGTTTATAAT	10	36	1
          ****** **   **
MAP Score: 10.6145

Motif 6
ACGTGGTTATTTACCTTCCTTAAGGAATTTT	2	205	1
ATTAAAATATAAAAATTCCTTAATAATTTTA	8	39	1
TTAAAATCATAAAAATTCCTTAAGGAAGGTA	2	216	0
GGGAATTACCTTAATTCCCTTCATACTCCTC	9	125	0
CTCTACCTCCTAACCTTCTTTAAAGGTTTAT	3	41	0
ACTTTAATAATTATATTCCTTCGGTGAATGG	6	255	1
CGCCTCGTAATATCATTCTTTCTT       	5	116	1
ATAAGTATAATATATTTCTTTAGTTAGGGGG	4	100	0
ATTTCTTGAGAAAAGTTCTTTCTATAAGTAT	4	123	0
GCGGGGGACTTAAAATCCCCTGGGCGAAAAG	4	50	0
AGTTCGAGGGAAATTTTCCTTTTGACTCCGA	6	153	1
CTTCTGAGTATCTCTTCCCTTCGCTTTTGTT	9	48	1
       CCTTTACCTCCTTTGCGAAGGTTT	10	3	1
TTTAAATTATACTACTTCCTTTAGACATTAG	10	31	1
TTCCCTTCGCTTTTGTTCCTTTCTGTACTTG	9	62	1
ACCCGAAATTATAAGTACCTTGCAAGAAGTA	2	62	0
          **** ******
MAP Score: 9.68956

Motif 7
AAAATCTGTACCCTGCGGAGTTCGAAGAAAAAGA	2	97	1
GGGCGAAAAGCCCGTGAGGGTTCGACTCCCTCCA	4	26	0
TTCCTTTTGACTCCGAGGGTATCCACAAGGGCTG	6	168	1
TAGACAGCGCCTGCGGCGGGCACGGGCAGTGTAC	2	31	1
AAGCTCAAGACTCTTGAGGGCTTCCTCTTCATCC	6	53	1
          CTCCTTTGAGTTTGATTTTTTAAA	5	0	1
GAAAGCCTCTCCGTTTCGGGATCCATGCCGTTTT	2	142	0
GAGTAATTGCCTGAGAAGATTTCCCCGCCTCGTA	5	91	1
AAGATAAGGACTCCGAGGAGTATGAAGGGAATTA	9	111	1
TTTACAGGTTCTGGCATGAGTTCGAGGGAAATTT	6	135	1
TTCTATTCTTCTTAGCAGGTTTTGCATTCGGATT	9	180	0
GGAAGAGATACTCAGAAGGTATTACGAGGACCTT	9	32	0
GGGCTTTTCGCCCAGGGGATTTTAAGTCCCCCGC	4	47	1
          *** *  *** ***
MAP Score: 7.30653

Motif 8
TAATTTCGGGTTCCGAAAATCTGTACCCTGCGGAGTTCGAA	2	82	1
AAGGTAAATAACCACGTCGCCTTTTCCGTTCAGTTTAGCCT	2	181	0
AGTTTGATTTTTTAAACTAAGTTTAGCTTACGATTATTAAG	5	18	1
TACGTACTTGTACACGTTGGGTTTGCCATACAAAAGCTGGA	6	84	0
CTGGCATGAGTTCGAGGGAAATTTTCCTTTTGACTCCGAGG	6	145	1
TCCGAGGGTATCCACAAGGGCTGTTCCGTCCTCGTAAACTT	6	179	1
TCGTAATACCTTCTGAGTATCTCTTCCCTTCGCTTTTGTTC	9	39	1
TTTTCTATTCTTCTTAGCAGGTTTTGCATTCGGATTTCTCT	9	175	0
          * *  *  *  * * ** * *
MAP Score: 5.36713