AlignACE 3.0 10/20/99
AlignACE2 -i PA/PA_operons006_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944249345
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	korD	300	PAB0341
#1	iorA-2	67	PAB0718
#2	ftsZ-2	300	PAB0851
#3	soj	48	PAB0852
#4	PAB0854	99	hypothetical protein
#5	PAB1474	28	PAB1474
#6	PAB1471	28	PAB1471
#7	PAB1470	226	PAB1470

Motif 1
CAGGGAATTGTGCCTAGAATCCATGAACTG	0	250	1
AATACTTTTTGGCCTAAATTATTTTTGTGA	2	16	0
TTAAAGGCTAGGCTTAGAATAGGGAATTTC	2	53	1
TTGTAGGAATGGCCAAGATGAAAATAATAA	2	94	1
TTTAATTCATGGCCTAGATTCTCTTGTTAA	2	143	1
AAGATAATAGGGCCTAAATGGATGAAGATA	7	28	0
TCATAGGTAATGCCAAAATTTGACAATTGT	7	109	1
          **********
MAP Score: 9.67266

Motif 2
ACCCTGGGATCAAGAACAAAACCATTGTAGTG	0	43	0
GCCCAAAACCCCAGGAGAAAACAAAAACTAAA	0	93	1
GGAGCGAAGAACAGATGAAAATTTTTTCGTGT	0	133	0
TAGGAATGGCCAAGATGAAAATAATAAGCGTC	2	97	1
TCCAACTTCCCCAGAATTTAATTCATGGCCTA	2	127	1
AGGAGCTATACAAGGAGGAAATCCAGGAAGAA	2	235	1
AGGAGGAAATCCAGGAAGAAATCCCCGAATAC	2	247	1
CATTGATGTTCAAGAAATAAATTAGTGAAA  	4	8	0
TTCAAAAATTCAAGATTGAACTCGGATTAATT	7	181	1
          ******  ****
MAP Score: 9.00511

Motif 3
AAACCCGTAACACGAAAAAATTTTCATCTGTTC	0	124	1
   ATATTATCACAAAAATAATTTAGGCCAAAA	2	7	1
ATAATTTAGGCCAAAAAGTATTTAACTAATTAA	2	24	1
TCCAACTTCCCCAGAATTTAATTCATGGCCTAG	2	127	1
TTCACTCCCCCCAAAATTTATCTAACAACGTAT	2	275	0
       TTTCACTAATTTATTTCTTGAACATC	4	3	1
ATTTCTTGAACATCAATGTATCTTTGAGAGGAT	4	22	1
 ATCACACCACCCCAAAATAATTAATAAA    	5	6	0
CCGAAAACTACATAAATCAAATTCAAAAATTCA	7	160	1
          **  *** *****
MAP Score: 7.70765

Motif 4
GTTTTGTTCTTGATCCCAGGGTCGAGCGTA	0	53	1
AAAATGCCCAAAACCCCAGGAGAAAACAAA	0	88	1
GTATCCTTGCTAATTCCAGGGAATTGTGCC	0	234	1
TAACTTTCACTAATCCCAGACGGAGGGGTT	1	44	1
AGTATTTAACTAATTAAAGGCTAGGCTTAG	2	40	1
CCCCAGAATTTAATTCATGGCCTAGATTCT	2	135	1
TACAAGGAGGAAATCCAGGAAGAAATCCCC	2	243	1
ATCCAGGAAGAAATCCCCGAATACGTTGTT	2	255	1
GGATGAAGATAAACTCAAGGTGATGAGTA 	7	9	0
TCAAATTCAAAAATTCAAGATTGAACTCGG	7	176	1
          **********
MAP Score: 6.22905

Motif 5
AATTTGAAATAATCCACTACAATGGTTTTG	0	29	1
GTAAAGTAAAAATGCCCAAAACCCCAGGAG	0	80	1
TTGTGCCTAGAATCCATGAACTGGACATTA	0	257	1
AACTTTCACTAATCCCAGACGGAGGGGTTA	1	45	1
ACAAGGAGGAAATCCAGGAAGAAATCCCCG	2	244	1
TCCAGGAAGAAATCCCCGAATACGTTGTTA	2	256	1
TGTCATAGGTAATGCCAAAATTTGACAATT	7	107	1
ACATAAATCAAATTCAAAAATTCAAGATTG	7	169	1
          **********
MAP Score: 2.69324

Motif 6
AAAGTTATATGGAGCGAAGAACAGATGAAAATTTTTTC	0	137	0
GGATATTTAGGGATCGTAGAGCGTTCCACGCATATTCA	0	176	0
TATGTCGGCCGTATCCTTGCTAATTCCAGGGAATTGTG	0	224	1
ATTGTGCCTAGAATCCATGAACTGGACATTAATGTTCA	0	256	1
CTTATTATTTTCATCTTGGCCATTCCTACAACACCCTT	2	87	0
TTTAACAAGAGAATCTAGGCCATGAATTAAATTCTGGG	2	136	0
GTATTTATCCGAATAGAAGCGAAGCCATCAGAGTAGCC	2	178	1
TTCTAAAGAAGGAGCTATACAAGGAGGAAATCCAGGAA	2	226	1
GAACATCAATGTATCTTTGAGAGGATCAAGGTCTAAGA	4	29	1
GTATAATGCGTTATCGACGATAGTCGATTGTCATAGGT	7	79	1
CGTAACGCTTTGAGCTTAGCACCGAAAACTACATAAAT	7	139	1
          * *** * ** * *   *
MAP Score: 1.03019

Motif 7
AAAAGTTATATGGAGCGAAGAACAGATGAAAAT	0	143	0
TGAATATGCGTGGAACGCTCTACGATCCCTAAA	0	176	1
CATGGATTCTAGGCACAATTCCCTGGAATTAGC	0	242	0
TAAAGGGTGTTGTAGGAATGGCCAAGATGAAAA	2	85	1
CTTCTAAAGAAGGAGCTATACAAGGAGGAAATC	2	225	1
GAGCTATACAAGGAGGAAATCCAGGAAGAAATC	2	237	1
GAGGAAATCCAGGAAGAAATCCCCGAATACGTT	2	249	1
AAGATCGCTTAGGAAGCATTTACTGGTGAAGCA	4	75	1
CTTAACTTTTTGGAGGGATATCC          	6	15	1
          ****** **  **
MAP Score: 1.02308

Motif 8
          AAACTCTAAGAGTCAATTAAAT	0	0	1
AAAATGCCCAAAACCCCAGGAGAAAACAAAAA	0	88	1
CGTTCCACGCATATTCAAAAAGTTATATGGAG	0	161	0
TAACTTTCACTAATCCCAGACGGAGGGGTTAA	1	44	1
AAAAATAATTTAGGCCAAAAAGTATTTAACTA	2	20	1
TTAACTAATTAAAGGCTAGGCTTAGAATAGGG	2	45	1
TGTTGTAGGAATGGCCAAGATGAAAATAATAA	2	92	1
AATTTAATTCATGGCCTAGATTCTCTTGTTAA	2	141	1
TACAAGGAGGAAATCCAGGAAGAAATCCCCGA	2	243	1
TGAGAGGATCAAGGTCTAAGAAATCTTATAAG	4	46	1
ATCCCTCCAAAAAGTTAAGAAGAA        	6	2	0
GGATGAAGATAAACTCAAGGTGATGAGTA   	7	7	0
TAAAGATAATAGGGCCTAAATGGATGAAGATA	7	28	0
TTTCGGTGCTAAGCTCAAAGCGTTACGACAAT	7	134	0
TCAAATTCAAAAATTCAAGATTGAACTCGGAT	7	176	1
GGATTAATTGAAAGCTTAAGGGGGCAGAAAAG	7	204	1
          ****** *** *
MAP Score: 0.76449