AlignACE 3.0 10/20/99
AlignACE2 -i AP/AP_operons026_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944249779
 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	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
TACTCTGCTAATATCCTTCCACTACTCATT	3	20	0
CTAAACAGGTCTAAACTTCCCTGGGCAGAG	3	85	0
CAGCTTATCACAAAACATCCACAGGCCTCA	3	146	1
          **********
MAP Score: 10.4261

Motif 2
TACGTCAAGAGGGGCGACGGCTGGTATGTGA	0	22	1
TTCAAGAACCGGCCCCAGGACAGCCCCGAGA	0	64	1
CCCCAGGACAGCCCCGAGAGGTATCTTATAG	0	76	1
TCTTATAGTGGGGCCGAAGAGGAGGGAGGCG	0	99	1
GAGGAGGGAGGCGCCCATAACCTTCCAGGTT	0	117	1
ATAGGTTAGAGGCTAGATAAGCTAGAGTAAA	1	45	1
AAACTTCCCTGGGCAGAGGGATCTTGGTGGG	3	72	0
CTCAGACGGCGGGCCGAGAGGTTGCTGCACT	3	178	1
          ******* ***
MAP Score: 8.3151

Motif 3
GCAAGTACGTGTACGTCAAGAGGGGCGACGGCT	0	11	1
TGAAGGTTAGGGTGTTCAAGAACCGGCCCCAGG	0	50	1
GGCCCCAGGACAGCCCCGAGAGGTATCTTATAG	0	74	1
ATCTTATAGTGGGGCCGAAGAGGAGGGAGGCGC	0	98	1
CATAACCTTCCAGGTTCTAGAGGAGG       	0	132	1
TTAAGAGTTAGCGGACGAAGATCGTTCCACAGC	2	57	0
GACTCAGACGGCGGGCCGAGAGGTTGCTGCACT	3	176	1
          * ** ** *****
MAP Score: 6.03291

Motif 4
TACCAGCCGTCGCCCCTCTTGACGTACACGTAC	0	15	0
GAACACCCTAACCTTCACATACCAGCCGTCGCC	0	34	0
GGGCGCCTCCCTCCTCTTCGGCCCCACTATAAG	0	100	0
CATTTACTCTAGCTTATCTAGCCTCTAACCTAT	1	45	0
TTCTATCTAAATCCCCTTTCGCTGTGGAACGAT	2	37	1
CTGTGGAACGATCTTCGTCCGCTAACTCTTAAC	2	58	1
GCTAACTCTTAACTTCCTAGGCTATATATAAAA	2	78	1
TACTCTGCTAATATCCTTCCACTACTCATTAAT	3	17	0
GCTCCCACCAAGATCCCTCTGCCCAGGGAAGTT	3	69	1
TTATCACAAAACATCCACAGGCCTCAGACTCAG	3	150	1
GTGCAGCAACCTCTCGGCCCGCCGTCTGAGTCT	3	175	0
          * **** ** ***
MAP Score: 5.31993

Motif 5
AGTACGTGTACGTCAAGAGGGGCGACGGCT	0	14	1
GTTCAAGAACCGGCCCCAGGACAGCCCCGA	0	63	1
GGCCCCAGGACAGCCCCGAGAGGTATCTTA	0	74	1
ATCTTATAGTGGGGCCGAAGAGGAGGGAGG	0	98	1
AAATGAAAATCATGCAAAGGGTCTTCTAA 	1	73	1
GATCGTTCCACAGCGAAAGGGGATTTAGAT	2	41	0
TAAACTTCCCTGGGCAGAGGGATCTTGGTG	3	74	0
TATCACAAAACATCCACAGGCCTCAGACTC	3	151	1
ACTCAGACGGCGGGCCGAGAGGTTGCTGCA	3	177	1
          **********
MAP Score: 4.74714

Motif 6
CCACTATAAGATACCTCTCGGGGCTGTCCTGG	0	78	0
GGGCGCCTCCCTCCTCTTCGGCCCCACTATAA	0	101	0
TTCTATCTAAATCCCCTTTCGCTGTGGAACGA	2	37	1
CTGTGGAACGATCTTCGTCCGCTAACTCTTAA	2	58	1
GCTAACTCTTAACTTCCTAGGCTATATATAAA	2	78	1
TACTCTGCTAATATCCTTCCACTACTCATTAA	3	18	0
GCTCCCACCAAGATCCCTCTGCCCAGGGAAGT	3	69	1
GGAAGTTTAGACCTGTTTAGGCATATCTTGCA	3	95	1
GCTGCTGTAAAAACGTTTAGGGTTGCAAGATA	3	118	0
   AGTGCAGCAACCTCTCGGCCCGCCGTCTG	3	180	0
          * ** *******
MAP Score: 2.22205