AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID048_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943391680
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	tap	45	methyl-accepting chemotaxis protein IV, peptide sensor receptor
#1	tar	144	methyl-accepting chemotaxis protein II, aspartate sensor receptor
#2	motA	126	proton conductor component of motor; no effect on switching
#3	flhD	300	regulator of flagellar biosynthesis, acting on class 2 operons; transcriptional initiation factor

Motif 1
TTTACTAACGCGGTCATTGCCGCCTGATGGGGAG	0	16	1
TTCAATTTCGCGGCGGGTGGCATCAGCAATAAAG	1	67	1
GTTATCGGCAAGGAGGGGGGAAACTTTATTGCTG	1	90	0
    CTGATACGGTGAGGCGCAACATTCCAGCAG	2	6	1
AAAAAAGCAGCGGTACGTCGTTACCGCTGCTGGA	2	32	0
GCACATACAACGGAGGGGGGCTGCGATTTTCAAT	3	62	0
TATTTTTTACCGGGGCTTCCCGGCGACATCACGG	3	235	1
GGCGACATCACGGGGTGCGGTGAAACCGCATAAA	3	256	1
          *** * *****  *
MAP Score: 9.6949

Motif 2
GCACATACAACGGAGGGGGGCTGCGATTTTCAAT	3	62	0
TTCAATTTCGCGGCGGGTGGCATCAGCAATAAAG	1	67	1
    CTGATACGGTGAGGCGCAACATTCCAGCAG	2	6	1
CCCGTGATGTCGCCGGGAAGCCCCGGTAAAAAAT	3	236	0
CATTGCCGCCTGATGGGGAGCGTTG         	0	30	1
GTTATCGGCAAGGAGGGGGGAAACTTTATTGCTG	1	90	0
CCCGGCGACATCACGGGGTGCGGTGAAACCGCAT	3	253	1
TGGTCAACAGTGGAAGGATGATGTC         	2	111	1
          *** **** **  *
MAP Score: 9.10057

Motif 3
TTTATTTCAATTTCGCGGCGGGTGGCATCA	1	62	1
GGGGAAACTTTATTGCTGATGCCACCCGCC	1	78	0
GGTACGTCGTTACCGCTGCTGGAATGTTGC	2	25	0
GGTAACGACGTACCGCTGCTTTTTTTTGCC	2	41	1
CATTATTGAAAATCGCAGCCCCCCTCCGTT	3	58	1
TGGTTCTGCTTATTGCAGCTTATCGCAACT	3	191	1
TATTGCAGCTTATCGCAACTATTCTAATGC	3	201	1
AATTATTTTTTACCGGGGCTTCCCGGCGAC	3	232	1
          **********
MAP Score: 8.35888

Motif 4
TCCCCATCAGGCGGCAATGACCGCGTTAGTAA	0	17	0
GATCTCGTTATCGGCAAGGAGGGGGGAAACTT	1	98	0
     CTGATACGGTGAGGCGCAACATTCCAG	2	5	1
CATTCCAGCAGCGGTAACGACGTACCGCTGCT	2	29	1
CAGTCGTCAGGCGTTAACGCGCGATTGGGGCA	2	67	0
TCTTAGATAAGTGTAAAGACCCATTTCTATTT	3	134	1
GTTGCGATAAGCTGCAATAAGCAGAACCACCT	3	188	0
CCGTGATGTCGCCGGGAAGCCCCGGTAAAAAA	3	237	0
ATCACGGGGTGCGGTGAAACCGCATAAAAATA	3	262	1
          **** ** ****
MAP Score: 8.12071

Motif 5
          CAACGCTCCCCATCAGGCGGCAAT	0	31	0
TTCAATTTCGCGGCGGGTGGCATCAGCAATAAAG	1	67	1
ATCAGCAATAAAGTTTCCCCCCTCCTTGCCGATA	1	88	1
TGGAATGTTGCGCCTCACCGTATCAG        	2	2	0
GCAGCGGTAACGACGTACCGCTGCTTTTTTTTGC	2	36	1
GCCCCAATCGCGCGTTAACGCCTGACGACTGAAC	2	68	1
TATTGAAAATCGCAGCCCCCCTCCGTTGTATGTG	3	61	1
CTGCTTATTGCAGCTTATCGCAACTATTCTAATG	3	196	1
TATTTTTTACCGGGGCTTCCCGGCGACATCACGG	3	235	1
TATGCGGTTTCACCGCACCCCGTGATGTCGCCGG	3	254	0
          *** ** ****  *
MAP Score: 4.64663

Motif 6
GCCGCCTGATGGGGAGCGTTG          	0	34	1
TTTCAATTTCGCGGCGGGTGGCATCAGCAAT	1	66	1
GTTATCGGCAAGGAGGGGGGAAACTTTATTG	1	93	0
ACTTGTTTTCAGGAAGGTGCCTT        	1	131	1
     CTGATACGGTGAGGCGCAACATTCCA	2	5	1
AAAAAAAGCAGCGGTACGTCGTTACCGCTGC	2	36	0
CAACAGTGGAAGGATGATGTC          	2	115	1
ATACAACGGAGGGGGGCTGCGATTTTCAATA	3	61	0
TTATTTTTTACCGGGGCTTCCCGGCGACATC	3	234	1
GCGACATCACGGGGTGCGGTGAAACCGCATA	3	257	1
          **** ******
MAP Score: 2.71253

Motif 7
TATTTACTAACGCGGTCATTGCCGCCTGATGGGGAG	0	14	1
GAAATGAACCCGATGATCTGCGCATCGGGTTTTTTA	1	30	1
ATTTCAATTTCGCGGCGGGTGGCATCAGCAATAAAG	1	65	1
TCGTTATCGGCAAGGAGGGGGGAAACTTTATTGCTG	1	90	0
      CTGATACGGTGAGGCGCAACATTCCAGCAG	2	4	1
CGACTGAACATCCTGTCATGGTCAACAGTGGAAGGA	2	93	1
ATTGAGTGTTTTGTGTGATCTGCATCACGCATTATT	3	29	1
CATCACGCATTATTGAAAATCGCAGCCCCCCTCCGT	3	51	1
CGTGTAGTGACGAGTACAGTTGCGTCGATTTAGGAA	3	95	1
AAAAAGGTGGTTCTGCTTATTGCAGCTTATCGCAAC	3	184	1
TGCTAATTATTTTTTACCGGGGCTTCCCGGCGACAT	3	228	1
GGCGACATCACGGGGTGCGGTGAAACCGCATAAAAA	3	256	1
          *  **   ****** *
MAP Score: 2.11515

Motif 8
 CAACGCTCCCCATCAGGCGGCAATGACCGCGTTAGTA	0	18	0
     TTCTCCCGATTTCCTCAATTGAAATGAACCCGA	1	5	1
ATGCCACCCGCCGCGAAATTGAAATAAAAAACCCGATG	1	52	0
TAAAGTTTCCCCCCTCCTTGCCGATAACGAGATCAACT	1	96	1
TGAGGCGCAACATTCCAGCAGCGGTAACGACGTACCGC	2	19	1
CTTTTTTTTGCCCCAATCGCGCGTTAACGCCTGACGAC	2	59	1
     GACATCATCCTTCCACTGTTGACCATGACAGGA	2	103	0
TTGAAAATCGCAGCCCCCCTCCGTTGTATGTGCGTGTA	3	63	1
CGTGATGTCGCCGGGAAGCCCCGGTAAAAAATAATTAG	3	230	0
          **      * *** ****
MAP Score: 0.72511