AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID024_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943391162
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	oppA	300	oligopeptide transport; periplasmic binding protein
#1	oppB	85	oligopeptide transport permease protein
#2	spr	300	putative lipoprotein
#3	rtn	180	orf, hypothetical protein
#4	yejA	75	orf, hypothetical protein
#5	yhhU	54	orf, hypothetical protein
#6	nikA	110	periplasmic binding protein for nickel
#7	dppB	300	dipeptide transport system permease protein 1
#8	dppA	300	dipeptide transport protein

Motif 1
GTACTTTCCGGGCAACCGCCAGACGATTCTT	0	30	1
GTGCAGGGTCCCAATCCGGGATTACACATGC	0	238	1
CAAGACCGCACCAATCGGGTAATCTCGAACT	2	110	1
ATCATTAGCCGCAATCCGGCATGCTTTCACT	4	37	0
ATAAGCGGAGCGCATCAGGCATTTTTGCCTT	7	29	0
GCGTTAACCGCGCATCCGGCATAAACAAAGC	7	118	1
GAGGCACAGCGCCACCGGGTATACAGATTGT	7	160	0
TGCGTGCAGCGCCATCCGGCAGCAATACTTC	7	191	1
TATAGTGACCCGCAGCCTGGAACTGCGTGTC	7	266	0
CGTCAATACAGCCAACCGGGATTTACACCAA	8	84	0
TGTAACAGTGCGGATCCTCCATAAAATGCCC	8	150	0
TAACGTTGACCCGACCGGGCAAAAAACAAAA	8	213	1
          **** ******
MAP Score: 18.6831

Motif 2
AAACAAAAAAGCACTGCCTAAGCAGTGCTTTCAGTT	3	51	0
ACCCGGTGGCGCTGTGCCTCTGCGTGCAGCGCCATC	7	171	1
TCTCGAACTCGTTTTGCCTCGGCGGTAGATTATCCT	2	132	1
CCGTTTGGATGCAATCCCTTGGCTATCCTGACGAGT	3	14	1
GCATCAGGCATTTTTGCCTTTGCCATCAGTCTTGTA	7	13	0
CAGTGGGTTGTCGCTGCCTGACCTTTTTTGTTTTTT	8	233	0
 TGCCCTACCTTCTGGCCTGTGCCTTCTGTAATGCG	1	60	0
GCAGAAAGTCTCCGAGCCTGTGCAGGGTCCCAATCC	0	219	1
CAGCAATACTTCATTCCCTGTCCGATAAGGGCGGGA	7	210	1
TGTTTGTTGTTTTAACCCTTTGCAGTGGGTTGTCGC	8	255	0
TACCCGATTGGTGCGGTCTTGGCGAGCGGTTTTACA	2	95	0
GTCGATTCGTACTGTGTCTCCCCTGTCGAGACACAT	0	109	0
GACAAAGTGCGCTTTGTTTATGCCGGATGCGCGGTT	7	123	0
          **  *****  **  *
MAP Score: 13.9669

Motif 3
ACCAATAAAGAATCGTCTGGCGGTTGCCCGG	0	37	0
GCATGTGTAATCCCGGATTGGGACCCTGCAC	0	238	0
AGTTCGAGATTACCCGATTGGTGCGGTCTTG	2	110	0
GTAATCTCGAACTCGTTTTGCCTCGGCGGTA	2	128	1
ATTAGTCTCGTGTCGCTTGGCATTTTTTTAT	2	237	1
        TAAACCGTTTGGATGCAATCCCT	3	2	1
GTTTGGATGCAATCCCTTGGCTATCCTGACG	3	16	1
AGTGAAAGCATGCCGGATTGCGGCTAATGAT	4	37	1
ATAGATGGGCAGTCGGGTGGGCGGA      	6	4	0
CATCTATTTTAATCCATTGGGGTTACC    	6	93	1
ACAATCTGTATACCCGGTGGCGCTGTGCCTC	7	160	1
GAAGTATTGCTGCCGGATGGCGCTGCACGCA	7	191	0
TTGGTGTAAATCCCGGTTGGCTGTATTGACG	8	84	1
TTTTGTTTTTTGCCCGGTCGGGTCAACGTTA	8	213	0
          ****** ****
MAP Score: 9.78349

Motif 4
TGTGCAGGGTCCCAATCCGGGATTACACATGCT	0	237	1
ACTTTAATTGACCAACCCCGCTTATTAACTTTC	2	35	1
GTTTCCGCGTCTTGATCCAGGCTATAGTCCGGT	3	108	1
CATCATTAGCCGCAATCCGGCATGCTTTCACTA	4	36	0
ATCGTCATACTTATTTCCGCCATCTATTTTAAT	6	73	1
GATAAGCGGAGCGCATCAGGCATTTTTGCCTTT	7	28	0
GATGCGCTCCGCTTATCAGGCCTACGAAAATTC	7	44	1
GCGGTTAACGCCTTATCCGGCCTACAAAATCGT	7	96	0
GGCGTTAACCGCGCATCCGGCATAAACAAAGCG	7	117	1
CTGCGTGCAGCGCCATCCGGCAGCAATACTTCA	7	190	1
GCTCACAAATCAATTCCCGCCCTTATCGGACAG	7	227	0
ATACAGACACGCAGTTCCAGGCTGCGGGTCACT	7	261	1
GGTCACTATAGAGAATCCGGGTT          	7	287	1
CACCGTTGGTGTAAATCCCGGTTGGCTGTATTG	8	79	1
ACCTCATAACGTTGACCCGACCGGGCAAAAAAC	8	207	1
          *   *********
MAP Score: 7.73137

Motif 5
TCTTTATTGGTAATGAGAATAATTAACAATTAAAGAG	0	57	1
AATTAACAATTAAAGAGCGTCGCGAAAGAATAATGTG	0	77	1
ATCGTCTGAATCACCAGAATAAATAAAGTCGGTGATA	0	153	1
AACGATAAAGTAACCTGACAGCAGAAAGTCTCCGAGC	0	199	1
TTACTGGTATTAACCAGCATGTGTAATCCCGGATTGG	0	248	0
CCAGTAATTATAATGAGGGAGTCCAAAAAACA     	0	278	1
TTGGCTATCCTGACGAGTTAACTGAAAGCACTGCTTA	3	32	1
TTTCCTGAAATTACGACAACATTTAAAAGATAACAAT	3	142	0
TTGCGGCTAATGATGAGTAAAAGGAAATCCG      	4	54	1
CCAGAACAGGTAATCAGTATGACGAATACTTAAAATC	6	39	1
TGCGCTCCGCTTATCAGGCCTACGAAAATTCTGCAAT	7	46	1
GGTTAACGCCTTATCCGGCCTACAAAATCGTGCAAAT	7	90	0
CTACAATCTGTCAACAGAATGTGAAAACGTCAATACA	8	105	0
CTCATAACGTTGACCCGACCGGGCAAAAAACAAAAAA	8	209	1
          * *****  *    ***
MAP Score: 6.06332

Motif 6
GAATAATGTGTCTCGACAGGGGAGACACAG	0	104	1
CGATAAAGTAACCTGACAGCAGAAAGTCTC	0	201	1
GCATGTGTAATCCCGGATTGGGACCCTGCA	0	239	0
TAATTGACCAACCCCGCTTATTAACTTTCT	2	39	1
GTTCGAGATTACCCGATTGGTGCGGTCTTG	2	110	0
        TAAACCGTTTGGATGCAATCCC	3	2	1
CTTTCAGTTAACTCGTCAGGATAGCCAAGG	3	30	0
AGTGAAAGCATGCCGGATTGCGGCTAATGA	4	37	1
   TCCGCCCACCCGACTGCCCATCTATTG	6	7	1
      GGTAACCCCAATGGATTAAAATAG	6	96	0
GCTTTGTTTATGCCGGATGCGCGGTTAACG	7	119	0
CAATCTGTATACCCGGTGGCGCTGTGCCTC	7	161	1
GAAGTATTGCTGCCGGATGGCGCTGCACGC	7	192	0
GACACGCAGTTCCAGGCTGCGGGTCACTAT	7	266	1
         AACCCGGATTCTCTATAGTGA	7	289	0
TTGGTGTAAATCCCGGTTGGCTGTATTGAC	8	84	1
CATAACGTTGACCCGACCGGGCAAAAAACA	8	211	1
AGGCAGCGACAACCCACTGCAAAGGGTTAA	8	250	1
          **********
MAP Score: 5.66428

Motif 7
ACTTCAAGGGAAAACAAACAAC         	2	288	1
CTGATGAATGAAAACAAAAAAGCACTGCCTA	3	67	0
CAGTATGACGAATACTTAAAATCGTCATACT	6	53	1
ATTTGTGAGCAATACAGACACGCAGTTCCAG	7	250	1
AAAGATTAAAAAAACTTCAAACAGCTATTTG	8	35	0
TGAAAACGTCAATACAGCCAACCGGGATTTA	8	90	0
GACCGGGCAAAAAACAAAAAAGGTCAGGCAG	8	225	1
GCAAAGGGTTAAAACAACAAACATCACAATT	8	268	1
          ****** ****
MAP Score: 4.8742

Motif 8
ATTGCATGCGTTTCACTCAATTGTACTTTAATT	2	11	1
     GTTGTTTGTTTTCCCTTGAAGTCCTTAA	2	282	0
AACCGTTTGGATGCAATCCCTTGGCTATCCTGA	3	12	1
CCGCCATCTATTTTAATCCATTGGGGTTACC  	6	89	1
CGCATCAGGCATTTTTGCCTTTGCCATCAGTCT	7	17	0
AATCGTGCAAATTCAATACATTGCAGAATTTTC	7	69	0
GTTTGAAGTTTTTTTAATCTTTGTGTGTGGATT	8	44	1
TTGTGTGTGGATTCTCACCGTTGGTGTAAATCC	8	64	1
ATGTTTGTTGTTTTAACCCTTTGCAGTGGGTTG	8	259	0
          *****  ** ***
MAP Score: 4.57411