AlignACE 3.0 10/20/99
AlignACE2 -i AA/AA_operons010_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944235235
 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
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 2
         ACTCTACCTCCTAACCTTCTTT	3	51	0
         CCTTTACCTCCTTTGCGAAGGT	10	1	1
ATGTGCTTGGCTATACCTTCTAAAGTTGTGG	6	220	0
TCCACAAGGGCTGTTCCGTCCTCGTAAACTT	6	189	1
CGACGTGGTTATTTACCTTCCTTAAGGAATT	2	203	1
       TTCCCTTACCTCTTTTGCAATTGG	0	35	0
          ACATACCTTCCTCTTTTTCCA	6	0	1
       TACCTCTTCCTCCAGAAAAGAGTT	8	3	1
GCCAATTCCGCCACACCCCCTAACTAAAGAA	4	85	1
TTCTGAGTATCTCTTCCCTTCGCTTTTGTTC	9	49	1
ACCACGTCGCCTTTTCCGTTCAGTTTAGCCT	2	181	0
GATTATTAAGATATACCTCTTTCCCGAAGAT	5	49	1
TTCCGAAAATCTGTACCCTGCGGAGTTCGAA	2	92	1
          ACCCACCTCCTGTTATTTTTT	2	289	0
GTTCGACTCCCTCCACCCCCACCACCCAACC	4	10	0
TTCGAGGGAAATTTTCCTTTTGACTCCGAGG	6	155	1
CTGTCTATTTCTATCCCGTTCCTGTAAA   	2	7	0
GACACGAAAGCCTCTCCGTTTCGGGATCCAT	2	150	0
          ** ********
MAP Score: 13.8524

Motif 3
GTACCCTGCGGAGTTCGAAGAAAAAGACAC	2	104	1
GAACGGAAAAGGCGACGTGGTTATTTACCT	2	191	1
CTTTAAAGAAGGTTAGGAGGTAGAGT    	3	47	1
TTGGGTGGTGGGGGTGGAGGGAGTCGAACC	4	12	1
TGTCATCTTCGGGAAAGAGGTATATCTTAA	5	54	0
GAAAGAATGATATTACGAGGCGGGGAAATC	5	108	0
ACAAAAGCTGGATGAAGAGGAAGCCCTCAA	6	66	0
GTTCTGGCATGAGTTCGAGGGAAATTTTCC	6	142	1
TTTTCCTTTTGACTCCGAGGGTATCCACAA	6	166	1
AGTTGTGGAAGTTTACGAGGACGGAACAGC	6	198	0
CTCTTTTCTGGAGGAAGAGGTA        	8	2	0
ACTCAGAAGGTATTACGAGGACCTTTGGGA	9	27	0
TAAAGATAAGGACTCCGAGGAGTATGAAGG	9	109	1
          **********
MAP Score: 12.7802

Motif 4
GATCCCGAAACGGAGAGGCTTTCGTGTCAGGCTAAA	2	153	1
TCAGGCTAAACTGAACGGAAAAGGCGACGTGGTTAT	2	179	1
GGGCTTTTCGCCCAGGGGATTTTAAGTCCCCCGCGT	4	47	1
AAATAATAGAAGAAATGGAAAAAGAGGAAGGTATGT	6	10	0
TTTACGAGGACGGAACAGCCCTTGTGGATACCCTCG	6	181	0
CCTCTTCCTCCAGAAAAGAGTTTGTGAATTAAAATA	8	12	1
AAGAGATACTCAGAAGGTATTACGAGGACCTTTGGG	9	28	0
ACTACAAGTACAGAAAGGAACAAAAGCGAAGGGAAG	9	61	0
TCCGAGGAGTATGAAGGGAATTAAGGTAATTCCCAC	9	122	1
TTTAAACCTTCGCAAAGGAGGTAAAGG         	10	1	0
          * *** ***  * * *
MAP Score: 6.19283

Motif 5
GGTTCCGAAAATCTGTACCCTGCGGAGTTCGAAGAAAAAGACAC	2	90	1
TGTCAGGCTAAACTGAACGGAAAAGGCGACGTGGTTATTTACCT	2	177	1
GGGTGGAGGGAGTCGAACCCTCACGGGCTTTTCGCCCAGGGGAT	4	23	1
GGGGATTTTAAGTCCCCCGCGTCTGCCAATTCCGCCACACCCCC	4	61	1
ACCTACGTTTACAGGTTCTGGCATGAGTTCGAGGGAAATTTTCC	6	128	1
GTGGAAGTTTACGAGGACGGAACAGCCCTTGTGGATACCCTCGG	6	180	0
CGCCATAAAGATAAGGACTCCGAGGAGTATGAAGGGAATTAAGG	9	104	1
TCCCACTATTAGGGCTACAGCTAAGAGAAATCCGAATGCAAAAC	9	152	1
AGTATAATTTAAACCTTCGCAAAGGAGGTAAAGG          	10	0	0
          *   *  * *  * * * * *  *
MAP Score: 5.52924

Motif 6
ATTGGCTCAGAAAATTATAACATAAATTTG     	0	5	0
    ACTCAAAATTTTATAGCTTTAGAATTTATTA	1	18	0
TCATTCACGAAAGTGTATACTAAAAAAATAACAGG	2	267	1
AGCACAGAAAATACCTATAATCTAACTT       	3	3	0
AGTTCTTTCTATAAGTATAATATATTTCTTTAGTT	4	106	0
TCTTCGGGAAAGAGGTATATCTTAATAATCGTAAG	5	44	0
ATAGCCAAGCACATGTCTACTTTAATAATTATATT	6	237	1
TCTTGACGTGAATTGTATATTTAAAAAGT      	7	29	1
TTATTAAGGAATTTTTATATTTTAATTCACAAACT	8	30	0
GTCTAAAGGAAGTAGTATAATTTAAACCTTCGCAA	10	22	0
          *   ***** * ***
MAP Score: 5.51213

Motif 7
GGTTATTTACCTTCCTTAAGGAATTTTTATGAT	2	209	1
TTAGTATACACTTTCGTGAATGATAATTCATTC	2	257	0
AGTATAATATATTTCTTTAGTTAGGGGGTGTGG	4	95	0
GAGAAAAGTTCTTTCTATAAGTATAATATATTT	4	114	0
         GATTTCTTGAGAAAAGTTCTTTCT	4	131	0
TTCTTCTATTATTTCTTCGAAAAGCTCAAGACT	6	32	1
TAATAATTATATTCCTTCGGTGAATGG      	6	259	1
     TACCTCTTCCTCCAGAAAAGAGTTTGTG	8	5	1
AATTATACTACTTCCTTTAGACATTAGTTTATA	10	35	1
          ******* **  *
MAP Score: 5.03818

Motif 8
ATAGACAGCGCCTGCGGCGGGCACGGGCAG	2	30	1
AAATCTGTACCCTGCGGAGTTCGAAGAAAA	2	98	1
AGAGTAATTGCCTGAGAAGATTTCCCCGCC	5	90	1
CTTGTGGATACCCTCGGAGTCAAAAGGAAA	6	167	0
ACTTCCACAACTTTAGAAGGTATAGCCAAG	6	216	1
TAATTATATTCCTTCGGTGAATGG      	6	262	1
CCTCGTAATACCTTCTGAGTATCTCTTCCC	9	37	1
GAATGCAAAACCTGCTAAGAAGAATAGAAA	9	185	1
          **********
MAP Score: 2.74831

Motif 9
TTATAAGTACCTTGCAAGAAGTACACTGCCCGTGC	2	50	0
TGGTTATTTACCTTCCTTAAGGAATTTTTATGATT	2	208	1
GAGAAAAGTTCTTTCTATAAGTATAATATATTTCT	4	112	0
ATAGAAAGAACTTTTCTCAAGAAATC         	4	129	1
AGATATACCTCTTTCCCGAAGATGACAAGTATCAG	5	57	1
ATTACGAGGACCTTTGGGAAGAATAAACTAATTAC	9	11	0
CCTTTCTGTACTTGTAGTAAGCGTACGCCATAAAG	9	79	1
 CCTTTACCTCCTTTGCGAAGGTTTAAATTATACT	10	9	1
          *****   *** * *
MAP Score: 1.12586

Motif 10
TTATCATTCACGAAAGTGTATACTAAAAAAATAACA	2	264	1
TACCTCTTTCCCGAAGATGACAAGTATCAGAGTAAT	5	62	1
TATGGCAAACCCAACGTGTACAAGTACGTAGTCACC	6	95	1
TACGTAGTCACCTACGTTTACAGGTTCTGGCATGAG	6	119	1
TATAGCCAAGCACATGTCTACTTTAATAATTATATT	6	236	1
  CCATTCACCGAAGGAATATAATTATTAAAGTAGA	6	252	0
GAGGACCTTTGGGAAGAATAAACTAATTACT     	9	5	0
ACCTCCTTTGCGAAGGTTTAAATTATACTACTTCCT	10	15	1
TTATTATAAACTAATGTCTAAAGGAAGTAGTATAAT	10	36	0
          *  * ** ** * ***
MAP Score: 1.04822