AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID020_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943391082
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	ybaD	90	orf, hypothetical protein
#1	ribH	88	riboflavin synthase, beta chain
#2	ribA	169	GTP cyclohydrolase II
#3	ribE	214	riboflavin synthase, alpha chain
#4	ribB	300	3,4 dihydroxy-2-butanone-4-phosphate synthase

Motif 1
CCTTTGTTGTATCGTCAGTTCAGGGTAAAATAGA	0	36	1
ATTTCCGTTAACCACCTGGTCAGGACGCCGT   	0	69	1
GCTAAAATCCGCCCCCCTGCGGGGCCATACTCGA	1	49	1
CATAACTGAAAACGCCAGTTCCAGGAAAAATTGA	2	39	1
TTATTTTGCCATAACGAGAAGGGGTTCACCTAAT	2	111	0
AGACTAAAAAGCCGCCTGAATGGGCAGCAAAAAG	3	40	1
GCAGGTGGAAAACGCCCTTACCAGTGAAGGGGTA	3	144	0
GAATCCGCTTATTCTCAGGGCGGGGCGAAATTCC	4	52	1
GAGTTGATTTACCGCCGGTGGGGAATTTCGCCCC	4	73	0
GTTCGCACCCAAAGCGCTCGCGGGCTTTCAACTG	4	106	0
GAACTCAAAGGACAGCAGATCCGGTGTAATTCCG	4	136	1
CCGGACTCTAACCGTCGGCCCCGGAATTACACCG	4	157	0
GCCGACGGTTAGAGTCCGGATGGGAGAGAGTAAC	4	172	1
TATAGCCAAAATAACGTGAGCGGGTCCATGCCCG	4	214	0
          * **** *  ****
MAP Score: 10.0279

Motif 2
ACGGCGTCCTGACCAGGTGGTTAACGGAAATCTATTTTA	0	61	0
         TCTCCCGGCTCGAAAGGGAAGCAGCGCACG	1	1	1
TTCGAGTATGGCCCCGCAGGGGGGCGGATTTTAGCATAA	1	45	0
GGGCGTTTTCCACCTGCTATTGTGCTGAACAGAATGTCT	3	161	1
ATTTCGCCCCGCCCTGAGAATAAGCGGATTCACTATAAC	4	44	0
TAACCGTCGGCCCCGGAATTACACCGGATCTGCTGTCCT	4	144	0
ATTCCGGGGCCGACGGTTAGAGTCCGGATGGGAGAGAGT	4	164	1
TATGCCGCCACTCCTAAGACTGCCCTGATTCTGGTAACC	4	246	1
          * ** *       ******
MAP Score: 9.03096

Motif 3
CCTTTGTTGTATCGTCAGTTCAGGGTAAAATAGATTT	0	36	1
GATTTCCGTTAACCACCTGGTCAGGACGCCGT     	0	68	1
       TCTCCCGGCTCGAAAGGGAAGCAGCGCACG	1	3	1
TCGAGTATGGCCCCGCAGGGGGGCGGATTTTAGCATA	1	46	0
CATAACTGAAAACGCCAGTTCCAGGAAAAATTGACAG	2	39	1
GAACGATCGACGCGTCGTGATTAGGTGAACCCCTTCT	2	92	1
GAGACTAAAAAGCCGCCTGAATGGGCAGCAAAAAGAA	3	39	1
ATTCTTACCCCTTCACTGGTAAGGGCGTTTTCCACCT	3	139	1
GAATCCGCTTATTCTCAGGGCGGGGCGAAATTCCCCA	4	52	1
AAAGCCCGCGAGCGCTTTGGGTGCGAACTCAAAGGAC	4	112	1
TCCGGACTCTAACCGTCGGCCCCGGAATTACACCGGA	4	155	0
GGGAGAGAGTAACGATTCTGTCGGGCATGGACCCGCT	4	193	1
          * ** * **   *** *
MAP Score: 8.34915

Motif 4
AAAATAGATTTCCGTTAACCACCTGGTCAGGACGCCGT   	0	62	1
TATGCTAAAATCCGCCCCCCTGCGGGGCCATACTCGAACCC	1	46	1
ACTGGCGTTTTCAGTTATGATTGTGGGACTTATCAAAAAGG	2	17	0
CACTGGTAAGGGCGTTTTCCACCTGCTATTGTGCTGAACAG	3	152	1
ATGCGTTGCTGCCGCTAATCATTAGCGTTATAGTGAATCCG	4	18	1
TTATAGTGAATCCGCTTATTCTCAGGGCGGGGCGAAATTCC	4	45	1
GTAAATCAACTCAGTTGAAAGCCCGCGAGCGCTTTGGGTGC	4	95	1
GGACAGCAGATCCGGTGTAATTCCGGGGCCGACGGTTAGAG	4	145	1
AACGATTCTGTCGGGCATGGACCCGCTCACGTTATTTTGGC	4	203	1
          **** *      * ***   *
MAP Score: 5.48174

Motif 5
CGGGGCCGACGGTTAGAGTCCGGATGGGAGAGA	4	168	1
CAGCAGATCCGGTGTAATTCCGGGGCCGACGGT	4	148	1
ACGTTATTTTGGCTATATGCCGCCACTCCTAAG	4	231	1
CTCAGGGCGGGGCGAAATTCCCCACCGGCGGTA	4	65	1
TAACGTGAGCGGGTCCATGCCCGACAGAATCGT	4	204	0
CGAAATATTATGCTAAAATCCGCCCCCCTGCGG	1	38	1
AAATCAACTCAGTTGAAAGCCCGCGAGCGCTTT	4	97	1
TTGACAGATTTGTGCCATTCCGTGAACGATCGA	2	69	1
AGAAGAAGCAGGGGAAATTCAGTCTATTGTAGC	3	72	1
          ****  * *****
MAP Score: 5.09124

Motif 6
ATATTATGCTAAAATCCGCCCCCCTGCGGG	1	42	1
TCGGGTTCGAGTATGGCCCCGCAGGGGGGC	1	59	0
          GAAATTCTCCAGATAATGCT	2	159	0
TGAGAGACTAAAAAGCCGCCTGAATGGGCA	3	36	1
ACAATAGACTGAATTTCCCCTGCTTCTTCT	3	72	0
ATAGCAGGTGGAAAACGCCCTTACCAGTGA	3	151	0
CGCCGGTGGGGAATTTCGCCCCGCCCTGAG	4	65	0
CAACTCAGTTGAAAGCCCGCGAGCGCTTTG	4	101	1
GTCGGCCCCGGAATTACACCGGATCTGCTG	4	148	0
TATTTTGGCTATATGCCGCCACTCCTAAGA	4	235	1
          **********
MAP Score: 4.67568

Motif 7
TTTGTTGTATCGTCAGTTCAGGGTAAAATAGAT	0	38	1
TTCCGTTAACCACCTGGTCAGGACGCCGT    	0	71	1
     TCTCCCGGCTCGAAAGGGAAGCAGCGCA	1	5	1
GAGTATGGCCCCGCAGGGGGGCGGATTTTAGCA	1	48	0
CGTGAACGATCGACGCGTCGTGATTAGGTGAAC	2	89	1
TCTTACCCCTTCACTGGTAAGGGCGTTTTCCAC	3	141	1
ATCCGCTTATTCTCAGGGCGGGGCGAAATTCCC	4	54	1
AGTTGATTTACCGCCGGTGGGGAATTTCGCCCC	4	73	0
CGACGGTTAGAGTCCGGATGGGAGAGAGTAACG	4	174	1
          ** * *** ****
MAP Score: 4.30778

Motif 8
AAAAGCGTTGCGCCTTTGTTGTATCGTCAGTTCAGGGTA	0	24	1
TTTCCGTTAACCACCTGGTCAGGACGCCGT         	0	70	1
     TCTCCCGGCTCGAAAGGGAAGCAGCGCACGAAAT	1	5	1
ATGCTAAAATCCGCCCCCCTGCGGGGCCATACTCGAACC	1	47	1
ATTAGGTGAACCCCTTCTCGTTATGGCAAAATAAGCCAA	2	111	1
GACTAAAAAGCCGCCTGAATGGGCAGCAAAAAGAAGAAG	3	41	1
TGCGTTGCTGCCGCTAATCATTAGCGTTATAGTGAATCC	4	19	1
TATAGTGAATCCGCTTATTCTCAGGGCGGGGCGAAATTC	4	46	1
          *****     * *  ** *
MAP Score: 1.14831

Motif 9
AACCACCTGGTCAGGACGCCGT        	0	78	1
        TCTCCCGGCTCGAAAGGGAAGC	1	2	1
CGAAAGGGAAGCAGCGCACGAAATATTATG	1	20	1
TATGCTAAAATCCGCCCCCCTGCGGGGCCA	1	46	1
  TTTCTTCCTTCGGGTTCGAGTATGGCCC	1	70	0
GTTCACCTAATCACGACGCGTCGATCGTTC	2	92	0
TGCTGCCCATTCAGGCGGCTTTTTAGTCTC	3	39	0
CCGCTTATTCTCAGGGCGGGGCGAAATTCC	4	56	1
GGGGCGAAATTCCCCACCGGCGGTAAATCA	4	73	1
CCGGTGTAATTCCGGGGCCGACGGTTAGAG	4	156	1
CTCTCTCCCATCCGGACTCTAACCGTCGGC	4	172	0
CAGGGCAGTCTTAGGAGTGGCGGCATATAG	4	243	0
          **********
MAP Score: 0.87964