AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID024_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943391092
 numcols =     	10
 undersample = 	1
 oversample = 	1

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

Motif 1
GCATGTGTAATCCCGGATTGGGACCCTGCACA	0	237	0
AGTGAAAGCATGCCGGATTGCGGCTAATGATG	3	37	1
GAAGTATTGCTGCCGGATGGCGCTGCACGCAG	5	190	0
TTTTGTTTTTTGCCCGGTCGGGTCAACGTTAT	6	212	0
ACAATCTGTATACCCGGTGGCGCTGTGCCTCT	5	160	1
TTCCCGCCCTTATCGGACAGGGAATGAAGTAT	5	215	0
AGACACGCAGTTCCAGGCTGCGGGTCACTATA	5	265	1
CGATTTTGTAGGCCGGATAAGGCGTTAACCGC	5	97	1
GTTGGTGTAAATCCCGGTTGGCTGTATTGACG	6	83	1
ATTTGGTACTTTCCGGGCAACCGCCAGACGAT	0	25	1
GCTTTGTTTATGCCGGATGCGCGGTTAACGCC	5	117	0
AGAATAATGTGTCTCGACAGGGGAGACACAGT	0	103	1
AAACAAAAAAGGTCAGGCAGCGACAACCCACT	6	236	1
ATAGATGGGCAGTCGGGTGGGCGGA       	4	3	0
CAGTTAACTCGTCAGGATAGCCAAGGGATTGC	2	24	0
AAGGCAAAAATGCCTGATGCGCTCCGCTTATC	5	29	1
AATTTTCGTAGGCCTGATAAGCGGAGCGCATC	5	44	0
          * ****** ***
MAP Score: 17.9992

Motif 2
ATAAAGAATCGTCTGGCGGTTGCCCGGAAAGTACCA	0	28	0
GCAGAAAGTCTCCGAGCCTGTGCAGGGTCCCAATCC	0	219	1
 TGCCCTACCTTCTGGCCTGTGCCTTCTGTAATGCG	1	60	0
CCGTTTGGATGCAATCCCTTGGCTATCCTGACGAGT	2	14	1
AAACAAAAAAGCACTGCCTAAGCAGTGCTTTCAGTT	2	51	0
GCATCAGGCATTTTTGCCTTTGCCATCAGTCTTGTA	5	13	0
GGATGCGCGGTTAACGCCTTATCCGGCCTACAAAAT	5	99	0
TGCGCTTTGTTTATGCCGGATGCGCGGTTAACGCCT	5	116	0
ACCCGGTGGCGCTGTGCCTCTGCGTGCAGCGCCATC	5	171	1
TGCGTGCAGCGCCATCCGGCAGCAATACTTCATTCC	5	191	1
CAGCAATACTTCATTCCCTGTCCGATAAGGGCGGGA	5	210	1
CAGTGGGTTGTCGCTGCCTGACCTTTTTTGTTTTTT	6	233	0
TGTTTGTTGTTTTAACCCTTTGCAGTGGGTTGTCGC	6	255	0
          **   **** ***  *
MAP Score: 12.4405

Motif 3
GTACTTTCCGGGCAACCGCCAGACGATTCTTT	0	30	1
AAAGTAACCTGACAGCAGAAAGTCTCCGAGCC	0	205	1
GTGCAGGGTCCCAATCCGGGATTACACATGCT	0	238	1
CATTACAGAAGGCACAGGCCAGAAGGTAGGGC	1	62	1
ATCATTAGCCGCAATCCGGCATGCTTTCACTA	3	36	0
      TCCGCCCACCCGACTGCCCATCTATT	4	4	1
TTTTGCCTTTGCCATCAGTCTTGTATGG    	5	6	0
ATAAGCGGAGCGCATCAGGCATTTTTGCCTTT	5	28	0
GCGTTAACCGCGCATCCGGCATAAACAAAGCG	5	118	1
GAGGCACAGCGCCACCGGGTATACAGATTGTT	5	159	0
TGCGTGCAGCGCCATCCGGCAGCAATACTTCA	5	191	1
CGTCAATACAGCCAACCGGGATTTACACCAAC	6	83	0
GTCAGGCAGCGACAACCCACTGCAAAGGGTTA	6	247	1
          **** *** ***
MAP Score: 12.4309

Motif 4
TGGCGGTTGCCCGGAAAGTACCAAATGCGGTTC	0	18	0
GATAAAGTAACCTGACAGCAGAAAGTCTCCGAG	0	202	1
TTATCGCATTACAGAAGGCACAGGCCAGAAGGT	1	56	1
AAGGCACAGGCCAGAAGGTAGGGCA        	1	70	1
TGACGAGTTAACTGAAAGCACTGCTTAGGCAGT	2	42	1
TGAAAGCATGCCGGATTGCGGCTAATGATGAGT	3	39	1
  TCCGCCCACCCGACTGCCCATCTATTGATCC	4	8	1
 CCATACAAGACTGATGGCAAAGGCAAAAATGC	5	9	1
CTTTGTTTATGCCGGATGCGCGGTTAACGCCTT	5	115	0
CAGATTGTTGACAAAGTGCGCTTTGTTTATGCC	5	135	0
AATCTGTATACCCGGTGGCGCTGTGCCTCTGCG	5	162	1
AGTATTGCTGCCGGATGGCGCTGCACGCAGAGG	5	187	0
ACACGCAGTTCCAGGCTGCGGGTCACTATAGAG	5	267	1
          ** ** ***** *
MAP Score: 10.0874

Motif 5
GAATCGTCTGGCGGTTGCCCGGAAAGTACCAAAT	0	25	0
TAACCTGACAGCAGAAAGTCTCCGAGCCTGTGCA	0	209	1
GCAGGAGTGTCCTGCTCCACGGTGTCTGATTTTT	1	24	1
   TGCCCTACCTTCTGGCCTGTGCCTTCTGTAA	1	64	0
GTTTCCGCGTCTTGATCCAGGCTATAGTCCGGTC	2	108	1
TGAAAGCATGCCGGATTGCGGCTAATGATGAGTA	3	39	1
GGCAAAAATGCCTGATGCGCTCCGCTTATCAGGC	5	31	1
TTTGTTTATGCCGGATGCGCGGTTAACGCCTTAT	5	113	0
ATCTGTATACCCGGTGGCGCTGTGCCTCTGCGTG	5	163	1
AAGTATTGCTGCCGGATGGCGCTGCACGCAGAGG	5	187	0
ATACAGACACGCAGTTCCAGGCTGCGGGTCACTA	5	261	1
       AACCCGGATTCTCTATAGTGACCCGCA	5	283	0
TGGTGTAAATCCCGGTTGGCTGTATTGACGTTTT	6	85	1
TTGTTTTTTGCCCGGTCGGGTCAACGTTATGAGG	6	208	0
ACCCTTTGCAGTGGGTTGTCGCTGCCTGACCTTT	6	243	0
          ** * * * *****
MAP Score: 8.0167

Motif 6
TTGGTACTTTCCGGGCAACCGCCAGACGATTCTTT	0	27	1
GATAAAGTAACCTGACAGCAGAAAGTCTCCGAGCC	0	202	1
ACAGAAGGCACAGGCCAGAAGGTAGGGCA      	1	66	1
GCTATCCTGACGAGTTAACTGAAAGCACTGCTTAG	2	35	1
ATAACAATGACCGGACTATAGCCTGGATCAAGACG	2	115	0
TCATCATTAGCCGCAATCCGGCATGCTTTCACTAT	3	35	0
         TCCGCCCACCCGACTGCCCATCTATT	4	1	1
TGATCCAGAACAGGTAATCAGTATGACGAATACTT	4	35	1
AAAATAGATGGCGGAAATAAGTATGACGATTTTAA	4	68	0
CTGATAAGCGGAGCGCATCAGGCATTTTTGCCTTT	5	28	0
AAGGCGTTAACCGCGCATCCGGCATAAACAAAGCG	5	115	1
ACAGCGCCACCGGGTATACAGATTGTTGACAAAGT	5	151	0
AACGTCAATACAGCCAACCGGGATTTACACCAACG	6	82	0
TGACCTACAATCTGTCAACAGAATGTGAAAACGTC	6	111	0
TTTGCCCGGTCGGGTCAACGTTATGAGGTGGGGAT	6	201	0
          **** ** * *  **
MAP Score: 7.43311

Motif 7
GGTTGCCCGGAAAGTACCAAATGCGGTTCTTACTCG	0	11	0
ATTACCAATAAAGAATCGTCTGGCGGTTGCCCGGAA	0	35	0
        TGGCAATACGTGGGGCAGGAGTGTCCTG	1	2	1
GATTTTTATCGCATTACAGAAGGCACAGGCCAGAAG	1	51	1
CATAGTGAAAGCATGCCGGATTGCGGCTAATGATGA	3	34	1
CAATAGATGGGCAGTCGGGTGGGCGGA         	4	1	0
      CCATACAAGACTGATGGCAAAGGCAAAAAT	5	4	1
GGCAAAGGCAAAAATGCCTGATGCGCTCCGCTTATC	5	25	1
TCAACAATCTGTATACCCGGTGGCGCTGTGCCTCTG	5	157	1
CCTCTGCGTGCAGCGCCATCCGGCAGCAATACTTCA	5	187	1
TACAGACACGCAGTTCCAGGCTGCGGGTCACTATAG	5	262	1
AAAAAACTTCAAACAGCTATTTGCAGCAGAGAAATT	6	22	0
CCGTTGGTGTAAATCCCGGTTGGCTGTATTGACGTT	6	81	1
GGCAAAAAACAAAAAAGGTCAGGCAGCGACAACCCA	6	230	1
          ***   * *  *****
MAP Score: 5.62302

Motif 8
CAGACGATCACCTTATGTCGATTCGTACTGTGTCTCCCCT	0	121	0
CAGGGTCCCAATCCGGGATTACACATGCTGGTTAATACCA	0	241	1
  TGCCCTACCTTCTGGCCTGTGCCTTCTGTAATGCGATA	1	57	0
CTAAGCAGTGCTTTCAGTTAACTCGTCAGGATAGCCAAGG	2	30	0
CATCAGAGAAAATGATGTTTCCGCGTCTTGATCCAGGCTA	2	92	1
AAGTATTCGTCATACTGATTACCTGTTCTGGATCAATAGA	4	30	0
CGCATCAGGCATTTTTGCCTTTGCCATCAGTCTTGTATGG	5	10	0
TACCCGGTGGCGCTGTGCCTCTGCGTGCAGCGCCATCCGG	5	170	1
GGTTGGCTGTATTGACGTTTTCACATTCTGTTGACAGATT	6	98	1
GCACTGTTACACTGATGTTAATTAGTACGGCATCCCCACC	6	170	1
ATCCCCACCTCATAACGTTGACCCGACCGGGCAAAAAACA	6	201	1
          * *   * *  * *** * *
MAP Score: 3.96764

Motif 9
AGGCAGTGCTTTTTTGTTTTCATTCATCAG	2	68	1
GTATGACGATTTTAAGTATTCGTCATACTG	4	53	0
AAATAGCTGTTTGAAGTTTTTTTAATCTTT	6	36	1
GTTGGCTGTATTGACGTTTTCACATTCTGT	6	99	1
TGCCTGACCTTTTTTGTTTTTTGCCCGGTC	6	225	0
ATTGTGATGTTTGTTGTTTTAACCCTTTGC	6	268	0
          **********
MAP Score: 2.0466

Motif 10
TGCTCCACGGTGTCTGATTTTTATCGCATTACAGAAGGCA	1	36	1
AATTCTGCAATGTATTGAATTTGCACGATTTTGTAGGCCG	5	72	1
GTCAACAATCTGTATACCCGGTGGCGCTGTGCCTCTGCGT	5	156	1
TTTTAATCTTTGTGTGTGGATTCTCACCGTTGGTGTAAAT	6	55	1
CCCGGTTGGCTGTATTGACGTTTTCACATTCTGTTGACAG	6	95	1
CTGCCTGACCTTTTTTGTTTTTTGCCCGGTCGGGTCAACG	6	216	0
CCAATTGTGATGTTTGTTGTTTTAACCCTTTGCAGTGGGT	6	261	0
          *** *     **  * * **
MAP Score: 0.982829