AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_fusions008_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241265
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF1045	86	methyl-accepting chemotaxis protein (tlpC-2)
#1	AF1049	102	type II secretion system protein (gspE-4)
#2	AF1052	32	A. fulgidus predicted coding region AF1052
#3	AF1053	34	A. fulgidus predicted coding region AF1053
#4	AF1055	111	flagellin (flaB1-2)
#5	AF1057	39	cytochrome C-type biogenesis protein (ccdA)
#6	AF1058	293	A. fulgidus predicted coding region AF1058
#7	AF1473	98	response regulator
#8	AF1475	109	mitochondrial benzodiazepine receptor/sensory transduction protein
#9	AF1484	87	A. fulgidus predicted coding region AF1484
#10	AF1898	74	response regulator
#11	AF2249	66	response regulator
#12	AF2251	30	competence-damage protein, putative
#13	AF2252	78	argininosuccinate synthetase (argG)

Motif 1
 TCCCCCAAATTTTTAATTTTTTAGAGGTGA	3	9	1
CAAATCACCCTTTTTAAATTTCCAGCACTCT	6	271	0
        TATTTTTAAATTTTTAAAATAAC	12	2	1
CCCAGGAAGTTTTTTAACTTTTGTTTAATCT	13	22	1
TATACATTTCTTTTTCAATTTTTATGCTTGA	5	17	1
AATGACTAAGTTTTTAAATTGCCAAGTCTAA	10	34	1
AAGAAAAGATTTTTTAACTTGTAAATTACAA	11	37	1
GAAAATTTTATTTTTTATTTTCGCAATCTAC	0	52	1
ATTTGGCGAGGTTTTAAATTTACGAGTGCTT	8	60	0
AGGGAATAATCTTTTAAGTTTTCTGTCAATT	9	18	0
ACACGAAAAATATTTAATTTTGAATGGGATA	7	45	1
TTGAAAGCGATTTTTCTTTTTTAAAAAGCAC	8	35	1
TCGCCAAATCTTTTATACTTTAAATTTAACT	8	82	1
GAGTCCATGTTTTTTCTTTTGGCCAGTGAAC	6	68	0
AAATTACCTTTTTCTAAGTTGAAATTTCCTT	4	19	0
CCTCACAAAATCTTTTATTTTCAAATAGCAA	9	57	1
          ******* ***
MAP Score: 27.2603

Motif 2
         ATCCTCCCCCCTTCATTATAATAA	1	88	0
    CGTAATACCTCAGCGCAGCCGCTCTCACG	2	13	0
    CCCATCACCTCTCACCTCATCCTCAAACT	4	92	0
TGAACCCGCGGCCTCCGCCTCGCGAAGGCGGCG	6	108	1
TCGTGTGATTACCGCTGCTCCGCCAACATAATC	7	18	0
    CTTCACACCTCTGATTATCCTGCGATTGA	7	79	0
TAAATTTAAAACCTCGCCAAATCTTTTATACTT	8	69	1
CCTTTCGGTGACCTCACAAAATCTTTTATTTTC	9	46	1
         TGCCTCGCCACAAAAAGGTATCGG	10	1	1
         AACCTCTGAAAACCCAGGAAGTTT	13	1	1
AAAGATTTAAACCTCTCCGCATGACGGGATTGT	13	55	1
          ***** ** ** *
MAP Score: 12.0786

Motif 3
TTTCGAATAAGAAAATTCAGAAGTGTAA       	0	3	0
TTTCTTATTCGAAATTTTACTTTATAGAGAAAATT	0	24	1
AAGGTGCAGTGTAATCCCAAAAATGAAAGCAAAGG	1	21	1
AAGGTTAATAGCAACATCAGTTGATAGTAGTAATA	1	52	1
TTACGTAAAGGAAATTTCAACTTAGAAAAAGGTAA	4	12	1
TTAGAAAAAGGTAATTTCAACATATAAGAAAATTC	4	33	1
TTTTTGATAAGGGAGTTCATAAAATTTTTTGAAAC	6	16	1
ACTTCAGAGGGAAACCTTAATATAGTCTTGAAAGA	6	237	1
AGAGAGTGCTGGAAATTTAAAAAGGGTGATTTGA 	6	269	1
TGGCGAGGTTTTAAATTTACGAGTGCTTTTTAAAA	8	53	0
TAAATTGACAGAAAACTTAAAAGATTATTCCCTTT	9	16	1
TTCCCTTTCGGTGACCTCACAAAATCTTTTATTTT	9	43	1
AGAACCTGGAGTAATTTCAAAACTGCAAGAAAAGA	11	11	1
   AACCTCTGAAAACCCAGGAAGTTTTTTAACTT	13	7	1
TAACTTTTGTTTAATCTCAAAAGATTTAAACCTCT	13	36	1
          * ** ****  * **
MAP Score: 9.04777

Motif 4
       TTACACTTCTGAATTTTCTTATT	0	3	1
        AACACCACCGAAAGTAGATTGC	0	74	0
     GGTATCACCTCTAAAAAATTAAAAA	3	19	0
     CCCATCACCTCTCACCTCATCCTCA	4	96	0
AAACCTTTATAACCCCTGAGGTCAAAAAGG	6	169	0
     CTTCACACCTCTGATTATCCTGCGA	7	83	0
TTTTAAAAAGCACTCGTAAATTTAAAACCT	8	53	1
   TTCCTGACACCTGTAAAAATTAGACTT	10	57	0
AAGATTTTTTAACTTGTAAATTACAATTGT	11	42	1
          AACCTCTGAAAACCCAGGAA	13	0	1
          **********
MAP Score: 6.64012

Motif 5
ACACTTCTGAATTTTCTTATTCGAAATTTT	0	12	1
CTTATTCGAAATTTTACTTTATAGAGAAAA	0	27	1
AAAATAAAAAATAAAATTTTCTCTATAAAG	0	43	0
AAAATTTTATTTTTTATTTTCGCAATCTAC	0	53	1
TGATGTTGCTATTAACCTTTGCTTTCATTT	1	41	0
TCCCCCAAATTTTTAATTTTTTAGAGGTGA	3	10	1
TCTAAGTTGAAATTTCCTTTACGTAATT  	4	8	0
ATATGTTGAAATTACCTTTTTCTAAGTTGA	4	28	0
TAAGAAAATTCTTATATATTGCTAATCGCT	4	57	1
     ATTTAAATATACATTTCTTTTTCAA	5	5	1
GAGTCCATGTTTTTTCTTTTGGCCAGTGAA	6	69	0
CTACGAGCCCTTGAACCTTTTTGACCTCAG	6	154	1
AATCACCCTTTTTAAATTTCCAGCACTCTC	6	270	0
CCCATTCAAAATTAAATATTTTTCGTGTGA	7	43	0
TTGAAAGCGATTTTTCTTTTTTAAAAAGCA	8	35	1
CGCCAAATCTTTTATACTTTAAATTTAACT	8	83	1
TATACTTTAAATTTAACTATACCC      	8	95	1
CCGAAAGGGAATAATCTTTTAAGTTTTCTG	9	24	0
GTGACCTCACAAAATCTTTTATTTTCAAAT	9	53	1
TACAAGTTAAAAAATCTTTTCTTGCAGTTT	11	30	0
      TATTTTTAAATTTTTAAAATAACT	12	4	1
CAGGAAGTTTTTTAACTTTTGTTTAATCTC	13	24	1
CGGAGAGGTTTAAATCTTTTGAGATTAAAC	13	44	0
          **********
MAP Score: 1.5851

Motif 6
CCGTGAGAGCGGCTGCGCTGAGGTATTACG  	2	12	1
TTTAGTTTGAGGATGAGGTGAGAGGTGATGGG	4	89	1
GCCTTCGCGAGGCGGAGGCCGCGGGTTCAAAT	6	105	0
GCCTCGCGAAGGCGGCGCTCTCCCGCTGAGCT	6	124	1
GGCGCTCTCCCGCTGAGCTACGAGCCCTTGAA	6	137	1
TGATTATGTTGGCGGAGCAGCGGTAATCACAC	7	17	1
          *********  *
MAP Score: 1.30726

Motif 7
GGCCGTGAGAGCGGCTGCGCTGAGGTATTA	2	10	1
GGTTTAGTTTGAGGATGAGGTGAGAGGTGA	4	87	1
CCGCCTTCGCGAGGCGGAGGCCGCGGGTTC	6	109	0
CCGCCTCGCGAAGGCGGCGCTCTCCCGCTG	6	122	1
GCGGCGCTCTCCCGCTGAGCTACGAGCCCT	6	135	1
GATTATGTTGGCGGAGCAGCGGTAATCACA	7	18	1
          **********
MAP Score: 0.0766425