AlignACE 3.0 10/20/99
AlignACE2 -i AP/AP_operons026_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944249789
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	APE0426	148	373aa long hypothetical dolichol-phosphate-mannosyltransferase
#1	APE1192	92	290aa long hypothetical dolichol monophosphate mannose synthase
#2	APE1193	104	195aa long hypothetical capsular synthesis regulator component B
#3	APE1194	111	104aa long hypothetical protein
#4	APE1195	300	186aa long hypothetical adenylylsulfate kinase
#5	APE1385_APE1386	199	APE1385: 219aa long hypothetical protein, APE1386: 423aa long hypothetical glutamate dehydrogenase

Motif 1
CTTGAACACCCTAACCTTCACATACCAGCC	0	40	0
GGAGGCGCCCATAACCTTCCAGGTTCTAGA	0	123	1
CATAGCAGATATAAACTTTCTATCTAAATC	2	20	1
TCCGCTAACTCTTAACTTCCTAGGCTATAT	2	75	1
CATATCTAAAATATCTTTCCTATACTAACA	3	44	0
GTCTTTTTTACTATCCTTACCGTATTAGGG	3	80	0
GTTCTCCTCTATAAACTTCCTAGCCTTCTC	4	56	1
CTCCTCCTGTCTAACCTGCCATCTGAATTA	4	138	1
GAAACTATTTATAACTATCCTAGGGTAATT	4	163	0
TACTCTGCTAATATCCTTCCACTACTCATT	5	20	0
CTAAACAGGTCTAAACTTCCCTGGGCAGAG	5	85	0
CAGCTTATCACAAAACATCCACAGGCCTCA	5	146	1
          **********
MAP Score: 18.2976

Motif 2
AGTACGTGTACGTCAAGAGGGGCGACGGCTGGTAT	0	14	1
TGGTATGTGAAGGTTAGGGTGTTCAAGAACCGGCC	0	43	1
ATAGTGGGGCCGAAGAGGAGGGAGGCGCCCATAAC	0	103	1
CATAGGTTAGAGGCTAGATAAGCTAGAGTAAATGA	1	44	1
TTTTATATATAGCCTAGGAAGTTAAGAGTTAGCGG	2	76	0
ATAATATGTTAGTATAGGAAAGATATTTTAGATAT	3	38	1
TGCCCTAATACGGTAAGGATAGTAAAAAAGACGTG	3	78	1
GGAAGTTTATAGAGGAGAACGGAGGGTTTAAGGAT	4	41	0
CTTTATGAGAAGGCTAGGAAGTTTATAGAGGAGAA	4	57	0
TTCAGATGGCAGGTTAGACAGGAGGAGGTGTTTCG	4	130	0
CCGGTGTTAGCGAGGAGGGCAGGCAACCGAGGATA	4	202	1
CAGGCAACCGAGGATAGACCGGAAAACAATATTAA	4	221	1
AGGACATGCACGGCTAGGCCTGACAGG        	4	283	1
TTTATTAATGAGTAGTGGAAGGATATTAGCAGAGT	5	14	1
GCTGTAAAAACGTTTAGGGTTGCAAGATATGCCTA	5	112	0
          *** ****  **  *
MAP Score: 16.2527

Motif 3
  GGCAAGTACGTGTACGTCAAGAGGGGCGACGGCT	0	8	1
TGAAGGTTAGGGTGTTCAAGAACCGGCCCCAGGACA	0	50	1
ATCTTATAGTGGGGCCGAAGAGGAGGGAGGCGCCCA	0	98	1
CATAACCTTCCAGGTTCTAGAGGAGG          	0	132	1
AGGGTTTAAGGATGTTTCCGAGCTGGTCGAGTTTCT	4	18	0
GATTTCCAGGGAGCTTTATGAGAAGGCTAGGAAGTT	4	69	0
GACAGGAGGAGGTGTTTCGCTATGGGTGATAAGGTA	4	113	0
ATTCAGATGGCAGGTTAGACAGGAGGAGGTGTTTCG	4	130	0
TAACTATCCTAGGGTAATTCAGATGGCAGGTTAGAC	4	146	0
GCTGGATTCCGGTGTTAGCGAGGAGGGCAGGCAACC	4	194	1
          *****    ***  **
MAP Score: 14.4649

Motif 4
      GGCAAGTACGTGTACGTCAAGAGGGGCGACGGCTGG	0	4	1
AAGAGGGGCGACGGCTGGTATGTGAAGGTTAGGGTGTTCAAG	0	28	1
GAGGTATCTTATAGTGGGGCCGAAGAGGAGGGAGGCGCCCAT	0	93	1
  CCTCCTCTAGAACCTGGAAGGTTATGGGCGCCTCCCTCCT	0	118	0
ATTGAGAGACAATATGACTATGCATAGGTTAGAGGCTAGATA	1	22	1
TATGATTAGCATAATATGTTAGTATAGGAAAGATATTTTAGA	3	28	1
GCTTTATGAGAAGGCTAGGAAGTTTATAGAGGAGAACGGAGG	4	51	0
GGTAATTCAGATGGCAGGTTAGACAGGAGGAGGTGTTTCGCT	4	128	0
GCGAGGAGGGCAGGCAACCGAGGATAGACCGGAAAACAATAT	4	211	1
ACAGCTAATAAGGACATGCACGGCTAGGCCTGACAGG     	4	273	1
GGCTCCCACCAAGATCCCTCTGCCCAGGGAAGTTTAGACCTG	5	68	1
          * ***  *   *   ***   *
MAP Score: 12.5862

Motif 5
        GGCAAGTACGTGTACGTCAAGAGGGGCGACGGCTGG	0	2	1
TCAAGAGGGGCGACGGCTGGTATGTGAAGGTTAGGGTGTTCAAG	0	26	1
AGGTATCTTATAGTGGGGCCGAAGAGGAGGGAGGCGCCCATAAC	0	94	1
AATATGACTATGCATAGGTTAGAGGCTAGATAAGCTAGAGTAAA	1	32	1
ACGGTAAGGATAGTAAAAAAGACGTGTAGATCGG          	3	87	1
       CGTTCAGGAGAAACTCGACCAGCTCGGAAACATCCTT	4	3	1
TTGAGATTTCCAGGGAGCTTTATGAGAAGGCTAGGAAGTTTATA	4	65	0
TTCCGCTGGATTCCGGTGTTAGCGAGGAGGGCAGGCAACCGAGG	4	190	1
TTACAGCTAATAAGGACATGCACGGCTAGGCCTGACAGG     	4	271	1
ACGGCTCCCACCAAGATCCCTCTGCCCAGGGAAGTTTAGACCTG	5	66	1
TTGTGATAAGCTGCTGTAAAAACGTTTAGGGTTGCAAGATATGC	5	115	0
ATCCACAGGCCTCAGACTCAGACGGCGGGCCGAGAGGTTGCTGC	5	162	1
          *   **      ** * ***   *
MAP Score: 11.4793

Motif 6
CACTATAAGATACCTCTCGGGGCTGTCCTGG	0	78	0
AGGCGCCCATAACCTTCCAGGTTCTAGAGGA	0	125	1
AGCAGATATAAACTTTCTATCTAAATCCCCT	2	23	1
GCTAACTCTTAACTTCCTAGGCTATATATAA	2	78	1
CTCCTCTATAAACTTCCTAGCCTTCTCATAA	4	59	1
CCTTCTCATAAAGCTCCCTGGAAATCTCAAT	4	79	1
CCTCCTGTCTAACCTGCCATCTGAATTACCC	4	140	1
AACAGGTCTAAACTTCCCTGGGCAGAGGGAT	5	81	0
  AGTGCAGCAACCTCTCGGCCCGCCGTCTG	5	180	0
          ******** **
MAP Score: 9.90933

Motif 7
 GGCAAGTACGTGTACGTCAAGAGGGGCGACGGCT	0	9	1
GTCAAGAGGGGCGACGGCTGGTATGTGAAGGTTAG	0	25	1
CCGGCCCCAGGACAGCCCCGAGAGGTATCTTATAG	0	72	1
GTATCTTATAGTGGGGCCGAAGAGGAGGGAGGCGC	0	96	1
TTAGATATGTGGCTGCCCTAATACGGTAAGGATAG	3	65	1
GGAGCTTTATGAGAAGGCTAGGAAGTTTATAGAGG	4	61	0
TAGGGTAATTCAGATGGCAGGTTAGACAGGAGGAG	4	138	0
CTGGATTCCGGTGTTAGCGAGGAGGGCAGGCAACC	4	195	1
ACCAAGATCCCTCTGCCCAGGGAAGTTTAGACCTG	5	75	1
AAAACGTTTAGGGTTGCAAGATATGCCTAAACAGG	5	106	0
CAGACTCAGACGGCGGGCCGAGAGGTTGCTGCACT	5	174	1
          * *  *** **** *
MAP Score: 8.72995

Motif 8
TTCACATACCAGCCGTCGCCCCTCTTGACGTAC	0	21	0
CCGGTTCTTGAACACCCTAACCTTCACATACCA	0	43	0
ACTATAAGATACCTCTCGGGGCTGTCCTGGGGC	0	75	0
        CCTCCTCTAGAACCTGGAAGGTTAT	0	133	0
CTAGCTTATCTAGCCTCTAACCTATGCATAGTC	1	37	0
TTCTATCTAAATCCCCTTTCGCTGTGGAACGAT	2	37	1
GCTAACTCTTAACTTCCTAGGCTATATATAAAA	2	78	1
TATTTTAGATATGTGGCTGCCCTAATACGGTAA	3	61	1
GTTCAGGAGAAACTCGACCAGCTCGGAAACATC	4	11	1
GCTCGGAAACATCCTTAAACCCTCCGTTCTCCT	4	31	1
CTCCTCTATAAACTTCCTAGCCTTCTCATAAAG	4	59	1
TAGCTACCTTATCACCCATAGCGAAACACCTCC	4	109	1
AAACACCTCCTCCTGTCTAACCTGCCATCTGAA	4	132	1
CTCGGTTGCCTGCCCTCCTCGCTAACACCGGAA	4	200	0
TCCCACCAAGATCCCTCTGCCCAGGGAAGTTTA	5	71	1
GTTTAGGCATATCTTGCAACCCTAAACGTTTTT	5	109	1
 AGTGCAGCAACCTCTCGGCCCGCCGTCTGAGT	5	177	0
          * *****  ****
MAP Score: 8.25246

Motif 9
CCGGTTCTTGAACACCCTAACCTTCACATA	0	46	0
GCCCCACTATAAGATACCTCTCGGGGCTGT	0	83	0
TTAGCGGACGAAGATCGTTCCACAGCGAAA	2	53	0
GCTAACTCTTAACTTCCTAGGCTATATATA	2	78	1
CCAGCTCGGAAACATCCTTAAACCCTCCGT	4	28	1
CTCCTCTATAAACTTCCTAGCCTTCTCATA	4	59	1
CCTTCTCATAAAGCTCCCTGGAAATCTCAA	4	79	1
ATACTCTGCTAATATCCTTCCACTACTCAT	5	21	0
GGCTCCCACCAAGATCCCTCTGCCCAGGGA	5	68	1
AACAGGTCTAAACTTCCCTGGGCAGAGGGA	5	82	0
          **********
MAP Score: 4.51986

Motif 10
GTCAAGAGGGGCGACGGCTGGTATGTGAAGGTTAGGGTGTTCAA	0	25	1
GTGTTCAAGAACCGGCCCCAGGACAGCCCCGAGAGGTATCTTAT	0	61	1
AAGAGGAGGGAGGCGCCCATAACCTTCCAGGTTCTAGAGGAGG 	0	115	1
ATCTTCGTCCGCTAACTCTTAACTTCCTAGGCTATATATAAAAC	2	68	1
TTAGATATGTGGCTGCCCTAATACGGTAAGGATAGTAAAAAAGA	3	65	1
    CGTTCAGGAGAAACTCGACCAGCTCGGAAACATCCTTAAA	4	6	1
AAACTTCCTAGCCTTCTCATAAAGCTCCCTGGAAATCTCAATAG	4	68	1
TGCCCTCCTCGCTAACACCGGAATCCAGCGGAAACTATTTATAA	4	179	0
CGAGGAGGGCAGGCAACCGAGGATAGACCGGAAAACAATATTAA	4	212	1
CAATATTAAAACAACATCTAGACATTACAGCTAATAAGGACATG	4	247	1
CAGCTAATAAGGACATGCACGGCTAGGCCTGACAGG        	4	274	1
AATACTGACGGCTCCCACCAAGATCCCTCTGCCCAGGGAAGTTT	5	59	1
TTATCACAAAACATCCACAGGCCTCAGACTCAGACGGCGGGCCG	5	150	1
          **   * *  * *     ***  *
MAP Score: 3.97797