AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_fusions001_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944240901
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF0438	79	3-ketoacyl-CoA thiolase (acaB-8)
#1	AF0439	82	transcriptional regulatory protein, AsnC family
#2	AF0442	300	succinoglycan biosynthesis regulator (exsB)
#3	AF0685	140	enoyl-CoA hydratase (fad-2)
#4	AF0968	205	3-ketoacyl-CoA thiolase (acaB-10)
#5	AF1025	150	3-hydroxyacyl-CoA dehydrogenase (hbd-4)
#6	AF1177	103	3-hydroxyacyl-CoA dehydrogenase (hbd-6)
#7	AF1191	32	dihydroxynaphthoic acid synthase (menB)
#8	AF1192	50	conserved hypothetical protein
#9	AF1195	27	activator 1, replication factor C, 53 KD subunit
#10	AF1196	65	N5,N10-methylenetetrahydromethanopterin reductase (mer-2)
#11	AF1197	300	3-ketoacyl-CoA thiolase (fadA-2)
#12	AF1208	165	conserved hypothetical protein
#13	AF1641	31	enoyl-CoA hydratase (fad-4)
#14	AF1642	50	histidyl-tRNA synthetase (hisS)
#15	AF2013	275	coenzyme F390 synthetase (ftsA-3)
#16	AF2014	63	sugar transporter, putative
#17	AF2426	85	conserved hypothetical protein
#18	AF2429	30	enoyl-CoA hydratase (fad-5)

Motif 1
GAACTAAATGCGGGGGGAGGGATTCGAACC	2	134	1
TGTCCCGTAGGGGTTCGAGGGTTCGAATCC	2	153	0
CATCTGAGCGGGGGTTGCCGAGCGGACAAA	2	202	0
GCTACCCCACGGGGGCGACGTGGAAAAATT	3	43	0
TCGCCCCCGTGGGGTAGCGGATATCCTGAG	3	55	1
GATATCCTGAGGGGCTGCGGACTCCTCGAC	3	74	1
GAGTTGAACCCGGGTCGAGGAGTCCGCAGC	3	87	0
AACTCCCGGCGGGGGCATGGAATTTTTAAT	3	112	1
ATGCTCAAAAGAGGCAGAGGCGGCAATGGT	6	18	1
AGTACAACATGGGCCTGAGGCCCGAGAAAG	6	73	1
GTTCAATGATGGGGCCGCCGAGATTTGAAC	15	86	1
GATTTGAACTCGGGTCACCGGCTCCCAAAG	15	107	1
TCATTACAGAGGGGCCGTAGGGTAGCCTGG	15	149	0
          **********
MAP Score: 15.328

Motif 2
ACGAAAACATTAAATATTACACGACTACTTT	0	53	1
ACTAAAAATATAAAAATTTTATGTTTGCCAT	1	48	0
TTATTGACATTAAAAATTCCATGCCCCCGCC	3	119	0
AACAAAAATATAAAAATAAAAAT        	4	2	0
AACAGCGTGTTAAAAACAAAAATATAAAAAT	4	16	0
ACATTAAAGCTAAATACAGTACGCTAAAAAC	4	44	0
TCTAAACGCGTAAAAATTGAATATATCAAGT	4	105	1
AAAAATTTCGTAAAAATAGTAAGAATTATAA	5	98	1
        ATTAAAAATTACAGCAAAATAGT	8	2	1
TTGGAAAAAATAAAAATTAAAA         	10	1	0
AAAGAAAAGGTAAATACTACAAATAGAAATT	12	10	0
AGGCAGGATTTAAATACTTCACCATCCTGAA	15	226	0
ATTAAAAAGCTAAAAATTTTATGCAAATAAA	16	29	0
          ******** **
MAP Score: 14.518

Motif 3
GAACAGAACTAAATGCGGGGGGAGGGATTCGAACCC	2	129	1
GGTCCTGTCCCGTAGGGGTTCGAGGGTTCGAATCCC	2	152	0
TTTTCATCTGAGCGGGGGTTGCCGAGCGGACAAAGG	2	200	0
ATCCGCTACCCCACGGGGGCGACGTGGAAAAATTGG	3	41	0
GTAGCGGATATCCTGAGGGGCTGCGGACTCCTCGAC	3	68	1
CCGGGAGTTGAACCCGGGTCGAGGAGTCCGCAGCCC	3	85	0
GGGTTCAACTCCCGGCGGGGGCATGGAATTTTTAAT	3	106	1
GAATATGCTCAAAAGAGGCAGAGGCGGCAATGGTTA	6	14	1
TCTCTGCTACCGTCGAGGTATCCGGGAGTTGT    	11	6	0
GGGGCCAGTGCCTTCCGGAAGTCCAGAACTTTCTCT	11	37	0
AAGGACGTAACGTTGAGGACGTGTTGAATAACAGCT	11	149	1
AAATTATCATCCCGGAGGAAGTCGAGTACACCGAAC	11	191	1
GCCAGTTCAATGATGGGGCCGCCGAGATTTGAACTC	15	82	1
GCTCCCAAAGCCGAGAGGATCACCAGGCTACCCTAC	15	127	1
TTAATCATTACAGAGGGGCCGTAGGGTAGCCTGGTG	15	147	0
TATCTTTCTGTCATGAGGGAGGCAGGATTTAAATAC	15	240	0
          **  ****  * ** *
MAP Score: 13.7564

Motif 4
TGAGGGTCCTGTCCCGTAGGGGTTCGAGGGT	2	161	0
GGGTAGCGGATATCCTGAGGGGCTGCGGACT	3	66	1
CCGGGTTCAACTCCCGGCGGGGGCATGGAAT	3	104	1
          CTCCGGGCAGGGAAAAATGTA	7	21	0
AATGAGAAATCTCCCTGTTGGCT        	10	52	1
AAGTTCTGGACTTCCGGAAGGCACTGGCCCC	11	42	1
TCTGCGTTATCACCCTGTAGGGGCCAGTGCC	11	61	0
GCTCTTAGCGCTTCATGAAGGACGTAACGTT	11	132	1
ACTCGACTTCCTCCGGGATGATAATTTCAAA	11	187	0
TAAAGAATTGGACCCGGATGGTATTTTAATA	11	255	1
   GCTCAAGCTTCGGCAAGGGTGTTTAAAA	14	32	0
CGCATTCGTTTTTCAGGATGGTGAAGTATTT	15	215	1
TAAATCCTGCCTCCCTCATGACAGAAAGATA	15	245	1
          ******** **
MAP Score: 10.5703

Motif 5
GAGCTGCAAGGCAAAATTCATATTTCACGAAAACATT	0	27	1
CATATTTCACGAAAACATTAAATATTACACGACTACT	0	45	1
CCATTTAATGGCAAACATAAAATTTTTATATTTTTAG	1	41	1
 AGTATGAAAGTAAACTAAAAATATAAAAATTTTATG	1	56	0
GATTTATCTTGCAAGAGTCCAATTTTTCCACGTCGCC	3	23	1
AACAGCGTGTTAAAAACAAAAATATAAAAATAAAAAT	4	10	0
AATTACGAGAGCAAATGAAAAATCTAAACGCGTAAAA	4	83	1
ATCTAAACGCGTAAAAATTGAATATATCAAGTATTAA	4	104	1
GGCACATTACGTAAAATTTAAGTATTAACGAA     	4	183	1
ATAAAATTGCGAAAGATTTAAAACTTTTCGGTAGGAG	5	17	0
AAAAATTACAGCAAAATAGTAATATATATGTTAATCA	8	13	1
CTATCTGTTGGAAAAAATAAAAATTAAAA        	10	2	0
GTTTTGATGAGCAAACGAAGAGAATGAAGCTCTTAGC	11	104	1
          GGAAATTTAAAGAATTAAAAAGCTAAA	16	46	0
TAGAGCTATGGGAAACGTCAAATAGCAGATTGCTGAA	17	50	1
          * ***  *  *** * *
MAP Score: 10.5677

Motif 6
ACAGAACTAAATGCGGGGGGAGGGATTCGAACCCT	2	131	1
TTTTCATCTGAGCGGGGGTTGCCGAGCGGACAAAG	2	201	0
CGCTACCCCACGGGGGCGACGTGGAAAAATTGGAC	3	39	0
AGCGGATATCCTGAGGGGCTGCGGACTCCTCGACC	3	70	1
GTTCAACTCCCGGCGGGGGCATGGAATTTTTAATG	3	108	1
TCAAAAGAGGCAGAGGCGGCAATGGTTAGGTTCTG	6	22	1
AAATTATCATCCCGGAGGAAGTCGAGTACACCGAA	11	191	1
AACCACCAACAAGAGAGGAAATCGACACACTTAAA	11	224	1
GCTCGTTTAAACGAGGTGTGGCTGATATGTAGAGT	12	69	1
TTAATCATTACAGAGGGGCCGTAGGGTAGCCTGGT	15	148	0
          * ******  *  **
MAP Score: 8.45767

Motif 7
GGCACTGGCCCCTACAGGGTGATAACGCAGATTGGTGT	11	61	1
ATCCGCTACCCCACGGGGGCGACGTGGAAAAATTGGAC	3	39	0
GGAGTTGAACCCGGGTCGAGGAGTCCGCAGCCCCTCAG	3	80	0
GCGGGGGTTGCCGAGCGGACAAAGGCGCAGGATTGAGG	2	187	0
        AGCCAACAGGGAGATTTCTCATTACTTATA	10	45	0
AGAACTAAATGCGGGGGGAGGGATTCGAACCCTCGAAC	2	133	1
GCTCCCAAAGCCGAGAGGATCACCAGGCTACCCTACGG	15	127	1
GGGTTCAACTCCCGGCGGGGGCATGGAATTTTTAATGT	3	106	1
TTGAAATTATCATCCCGGAGGAAGTCGAGTACACCGAA	11	188	1
GGGGCCAGTGCCTTCCGGAAGTCCAGAACTTTCTCTGC	11	35	0
TTTTAAACACCCTTGCCGAAGCTTGAGC          	14	32	1
AGTCCGCAGCCCCTCAGGATATCCGCTACCCCACGGGG	3	59	0
CCCGCCAGTTCAATGATGGGGCCGCCGAGATTTGAACT	15	79	1
CTCCCGGATACCTCGACGGTAGCAGAGAAAGTTCTGGA	11	14	1
          **  * *** *    ***
MAP Score: 8.11925

Motif 8
TCGCCCCCGTGGGGTAGCGGATATCCTGAGG	3	55	1
GATATCCTGAGGGGCTGCGGACTCCTCGACC	3	74	1
ATGCTCAAAAGAGGCAGAGGCGGCAATGGTT	6	18	1
AGTACAACATGGGCCTGAGGCCCGAGAAAGT	6	73	1
GGACTTCCGGAAGGCACTGGCCCCTACAGGG	11	49	1
ATTTGAACTCGGGTCACCGGCTCCCAAAGCC	15	108	1
GTAATGATTAAAGGCAGTGGCTTTTAAAGCC	15	172	1
          ******* ***
MAP Score: 4.67113

Motif 9
TACTTACACTTTAATTGCAATTAAAATTGCCAT	1	12	1
AAATTGCCATTTAATGGCAAACATAAAATTTTT	1	35	1
CATGGAATTTTTAATGTCAATAA          	3	127	1
AAACAGCGTGTTAAAAACAAAAATATAAAAATA	4	15	0
GTATTTAGCTTTAATGTCAATAATTAATTACGA	4	58	1
ATATCAAGTATTAATTGGAACAAATTCGGTACA	4	127	1
TACTTTGAAATTTATTTGAAAAAATTTCGTAAA	5	79	1
GGATGGTATTTTAATAAGAAAAAAGTGAAGGAG	11	270	1
AGCTAAAAATTTTATGCAAATAAATATGCATAA	16	20	0
          *****  *** **
MAP Score: 4.55215

Motif 10
TCATATTTCACGAAAACATTAAATATTACACGACTA	0	44	1
TAATGGCAAACATAAAATTTTTATATTTTTAGTTTA	1	46	1
GCGATGACTTCATATAACTTTGAAATCCACCTTCTA	2	273	1
AATCTAAACGCGTAAAAATTGAATATATCAAGTATT	4	103	1
CGGCACATTACGTAAAATTTAAGTATTAACGAA   	4	182	1
TGAACTCCTACCGAAAAGTTTTAAATCTTTCGCAAT	5	13	1
GAAATTTTTTCAAATAAATTTCAAAGTATGTCAAAT	5	71	0
TTTCTCATTACTTATACTTTAACTATCTGTTGGAAA	10	25	0
TCGCTCAACTCTAAAACCTTTTAAACACCCTTGCCG	14	14	1
TATTTATTTGCATAAAATTTTTAGCTTTTTAATTCT	16	27	1
          *  **** **  * **
MAP Score: 3.99518

Motif 11
GGAACACAGTAAGTTGAAATCAGACCAAAAT	2	11	1
CGGGGGGAGGGATTCGAACCCTCGAACCCCT	2	144	1
CGACGTGGAAAAATTGGACTCTTGCAAGATA	3	27	0
CCCCCGCCGGGAGTTGAACCCGGGTCGAGGA	3	96	0
CACACTTAAAGAATTGGACCCGGATGGTATT	11	249	1
CTGATATGTAGAGTCGAACCACATTGTATAA	12	90	1
GGGCCGCCGAGATTTGAACTCGGGTCACCGG	15	97	1
          ** ********
MAP Score: 3.93645

Motif 12
TTACACTTTAATTGCAATTAAAATTGCCATTTAATGGCA	1	15	1
AGTAAGTTGAAATCAGACCAAAATGGGATTGAAAGTGGA	2	18	1
TGAAAAATCTAAACGCGTAAAAATTGAATATATCAAGTA	4	98	1
ATCAAGTATTAATTGGAACAAATTCGGTACAGGCGGATT	4	129	1
CAAAATCTTAAATTGAGATAAAATTGCGAAAGATTTAAA	5	32	0
TATTTGAAAAAATTTCGTAAAAATAGTAAGAATTATAAA	5	91	1
     GGGGGAATATGCTCAAAAGAGGCAGAGGCGGCAA	6	5	1
    ATTAAAAATTACAGCAAAATAGTAATATATATGTT	8	6	1
TATGCAAATAAATATGCATAAAATGCACACT        	16	2	0
          ***      ***** *  *
MAP Score: 2.8174

Motif 13
AAATGCGGGGGGAGGGATTCGAACCCTCGAAC	2	139	1
TCATCTGAGCGGGGGTTGCCGAGCGGACAAAG	2	201	0
    GTAGAAGGTGGATTTCAAAGTTATATGA	2	282	0
GAATTATAAAGGAGGATTCCAAATATGAGTGG	5	120	1
TTATCATCCCGGAGGAAGTCGAGTACACCGAA	11	194	1
CACCAACAAGAGAGGAAATCGACACACTTAAA	11	227	1
          ** **** ****
MAP Score: 1.98703

Motif 14
CAGAACTAAATGCGGGGGGAGGGATTCGAA	2	132	1
TATTGTGGTTTAAAGGGCGATGACTTCATA	2	257	1
ACAAATTCGGTACAGGCGGATTATCTATTT	4	146	1
GTAAGAATTATAAAGGAGGATTCCAAATAT	5	116	1
CACTGGCCCCTACAGGGTGATAACGCAGAT	11	63	1
TAGCGCTTCATGAAGGACGTAACGTTGAGG	11	137	1
AAGAAAAAAGTGAAGGAGGTGTATT     	11	285	1
CTTTCTGTCATGAGGGAGGCAGGATTTAAA	15	243	0
          **********
MAP Score: 0.343837

Motif 15
CAACTCTACGCATAGAGCTGCAAGGCAAAATTCATA	0	13	1
GAACAGAACTAAATGCGGGGGGAGGGATTCGAACCC	2	129	1
GGTCCTGTCCCGTAGGGGTTCGAGGGTTCGAATCCC	2	152	0
GCGGGGGTTGCCGAGCGGACAAAGGCGCAGGATTGA	2	189	0
TCCGCTACCCCACGGGGGCGACGTGGAAAAATTGGA	3	40	0
TAGCGGATATCCTGAGGGGCTGCGGACTCCTCGACC	3	69	1
CCGGGAGTTGAACCCGGGTCGAGGAGTCCGCAGCCC	3	85	0
ACCCGGGTTCAACTCCCGGCGGGGGCATGGAATTTT	3	102	1
GGAATATGCTCAAAAGAGGCAGAGGCGGCAATGGTT	6	13	1
CATGCAGTACAACATGGGCCTGAGGCCCGAGAAAGT	6	68	1
TTGAAATTATCATCCCGGAGGAAGTCGAGTACACCG	11	188	1
ATTAAAATACCATCCGGGTCCAATTCTTTAAGTGTG	11	249	0
CCGAGATTTGAACTCGGGTCACCGGCTCCCAAAGCC	15	103	1
TTAATCATTACAGAGGGGCCGTAGGGTAGCCTGGTG	15	147	0
ATCTTTCTGTCATGAGGGAGGCAGGATTTAAATACT	15	239	0
          **   *** *  ****
MAP Score: 0.150103