AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID020_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943391029
 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
TGTTGTATCGTCAGTTCAGGGTAAAATAGA	0	40	1
CCGTTAACCACCTGGTCAGGACGCCGT   	0	73	1
        TCTCCCGGCTCGAAAGGGAAGC	1	2	1
CGAAAGGGAAGCAGCGCACGAAATATTATG	1	20	1
AAAATCCGCCCCCCTGCGGGGCCATACTCG	1	52	1
TTTGTGCCATTCCGTGAACGATCGACGCGT	2	77	1
GTTCACCTAATCACGACGCGTCGATCGTTC	2	92	0
ATTAGGTGAACCCCTTCTCGTTATGGCAAA	2	111	1
CTTTTTGCTGCCCATTCAGGCGGCTTTTTA	3	44	0
AACGCCCTTACCAGTGAAGGGGTAAGAATG	3	138	0
CCGCTTATTCTCAGGGCGGGGCGAAATTCC	4	56	1
GGGGCGAAATTCCCCACCGGCGGTAAATCA	4	73	1
CAGTTGAAAGCCCGCGAGCGCTTTGGGTGC	4	106	1
TCAAAGGACAGCAGATCCGGTGTAATTCCG	4	140	1
CCGGTGTAATTCCGGGGCCGACGGTTAGAG	4	156	1
CGTTACTCTCTCCCATCCGGACTCTAACCG	4	177	0
CGTGAGCGGGTCCATGCCCGACAGAATCGT	4	204	0
CGGGCATGGACCCGCTCACGTTATTTTGGC	4	214	1
GTTACCAGAATCAGGGCAGTCTTAGGAGTG	4	254	0
          **********
MAP Score: 10.3705

Motif 2
AAATAGATTTCCGTTAACCACCTGGTCAGGACGCCGT      	0	63	1
ATTTCGTGCGCTGCTTCCCTTTCGAGCCGGGAGA         	1	1	0
TTTCTTCCTTCGGGTTCGAGTATGGCCCCGCAGGGGGGCGGAT	1	55	0
TTAAGACATTCTGTTCAGCACAATAGCAGGTGGAAAACGCCCT	3	160	0
TATAGTGAATCCGCTTATTCTCAGGGCGGGGCGAAATTCCCCA	4	46	1
GGGCTTTCAACTGAGTTGATTTACCGCCGGTGGGGAATTTCGC	4	76	0
AGTTGAAAGCCCGCGAGCGCTTTGGGTGCGAACTCAAAGGACA	4	107	1
GACAGCAGATCCGGTGTAATTCCGGGGCCGACGGTTAGAGTCC	4	146	1
TTACCAGAATCAGGGCAGTCTTAGGAGTGGCGGCATATAGCCA	4	240	0
          * * *     *  ** * **  *
MAP Score: 10.346

Motif 3
CGGTGTAATTCCGGGGCCGACGGTTAGAGT	4	157	1
TATTCTCAGGGCGGGGCGAAATTCCCCACC	4	61	1
TGGCCCCGCAGGGGGGCGGATTTTAGCATA	1	46	0
TGATTTACCGCCGGTGGGGAATTTCGCCCC	4	73	0
CCGCCCCCCTGCGGGGCCATACTCGAACCC	1	57	1
AATAACGTGAGCGGGTCCATGCCCGACAGA	4	209	0
ACTGAAAACGCCAGTTCCAGGAAAAATTGA	2	43	1
CAGCACAATAGCAGGTGGAAAACGCCCTTA	3	158	0
TCAAAGGACAGCAGATCCGGTGTAATTCCG	4	140	1
TTTCTTCCTTCGGGTTCGAGTATGGCCCCG	1	68	0
      TCTCCCGGCTCGAAAGGGAAGCAG	1	4	1
CGGTTAGAGTCCGGATGGGAGAGAGTAACG	4	177	1
AAAAGAAGAAGCAGGGGAAATTCAGTCTAT	3	69	1
GGCAGTCTTAGGAGTGGCGGCATATAGCCA	4	240	0
GTTACCAGAATCAGGGCAGTCTTAGGAGTG	4	254	0
CCGTTAACCACCTGGTCAGGACGCCGT   	0	73	1
TGTTGTATCGTCAGTTCAGGGTAAAATAGA	0	40	1
GCGAGCGCTTTGGGTGCGAACTCAAAGGAC	4	119	1
GTAAATCAACTCAGTTGAAAGCCCGCGAGC	4	95	1
          **********
MAP Score: 9.75847

Motif 4
AAAATAGATTTCCGTTAACCACCTGGTCAGGACGCCGT	0	62	1
 TCTCCCGGCTCGAAAGGGAAGCAGCGCACGAAATATT	1	9	1
TATGCTAAAATCCGCCCCCCTGCGGGGCCATACTCGAA	1	46	1
TTTGTGCCATTCCGTGAACGATCGACGCGTCGTGATTA	2	77	1
GACATTCTGTTCAGCACAATAGCAGGTGGAAAACGCCC	3	161	0
TTATAGTGAATCCGCTTATTCTCAGGGCGGGGCGAAAT	4	45	1
GTAAATCAACTCAGTTGAAAGCCCGCGAGCGCTTTGGG	4	95	1
GGACAGCAGATCCGGTGTAATTCCGGGGCCGACGGTTA	4	145	1
AACGATTCTGTCGGGCATGGACCCGCTCACGTTATTTT	4	203	1
          ****       ** ****
MAP Score: 8.10398

Motif 5
TACAACAAAGGCGCAACGCTTTTGAGATAAAGGATCG    	0	6	0
AAATAGATTTCCGTTAACCACCTGGTCAGGACGCCGT    	0	63	1
ATTTCGTGCGCTGCTTCCCTTTCGAGCCGGGAGA       	1	3	0
ATGCTAAAATCCGCCCCCCTGCGGGGCCATACTCGAACCCG	1	47	1
CTGGCGTTTTCAGTTATGATTGTGGGACTTATCAAAAAGGA	2	16	0
ACATTCTGTTCAGCACAATAGCAGGTGGAAAACGCCCTTAC	3	157	0
TGCGTTGCTGCCGCTAATCATTAGCGTTATAGTGAATCCGC	4	19	1
TATAGTGAATCCGCTTATTCTCAGGGCGGGGCGAAATTCCC	4	46	1
AGTTGAAAGCCCGCGAGCGCTTTGGGTGCGAACTCAAAGGA	4	107	1
GACAGCAGATCCGGTGTAATTCCGGGGCCGACGGTTAGAGT	4	146	1
ACTCCTAAGACTGCCCTGATTCTGGTAACCATAATTTTAGT	4	255	1
          ****      ** ***    *
MAP Score: 7.04374

Motif 6
ATAGATTTCCGTTAACCACCTGGTCAGGACGCCGT      	0	65	1
TTCGTGCGCTGCTTCCCTTTCGAGCCGGGAGA         	1	1	0
TTCGAGTATGGCCCCGCAGGGGGGCGGATTTTAGCATAATA	1	43	0
AGACTAAAAAGCCGCCTGAATGGGCAGCAAAAAGAAGAAGC	3	40	1
AAGACATTCTGTTCAGCACAATAGCAGGTGGAAAACGCCCT	3	160	0
TAGTGAATCCGCTTATTCTCAGGGCGGGGCGAAATTCCCCA	4	48	1
CGCTTTGGGTGCGAACTCAAAGGACAGCAGATCCGGTGTAA	4	124	1
AGCAGATCCGGTGTAATTCCGGGGCCGACGGTTAGAGTCCG	4	149	1
          **  * *    **** *   *
MAP Score: 5.24035

Motif 7
AAAATAGATTTCCGTTAACCACCTGGTCAGGACGCC	0	62	1
        TCTCCCGGCTCGAAAGGGAAGCAGCGCA	1	2	1
TATGCTAAAATCCGCCCCCCTGCGGGGCCATACTCG	1	46	1
      TTTCTTCCTTCGGGTTCGAGTATGGCCCCG	1	68	0
CGACGCGTCGATCGTTCACGGAATGGCACAAATCTG	2	73	0
ATTAGGTGAACCCCTTCTCGTTATGGCAAAATAAGC	2	111	1
GGTGGGGAATTTCGCCCCGCCCTGAGAATAAGCGGA	4	55	0
GGGGCGAAATTCCCCACCGGCGGTAAATCAACTCAG	4	73	1
CAGTTGAAAGCCCGCGAGCGCTTTGGGTGCGAACTC	4	106	1
ACGGTTAGAGTCCGGATGGGAGAGAGTAACGATTCT	4	176	1
CGTGAGCGGGTCCATGCCCGACAGAATCGTTACTCT	4	198	0
          ****  * **   ***
MAP Score: 4.88122

Motif 8
AAAATAGATTTCCGTTAACCACCTGGTCAGGACGCCGT      	0	62	1
TAATATTTCGTGCGCTGCTTCCCTTTCGAGCCGGGAGA      	1	4	0
CACGAAATATTATGCTAAAATCCGCCCCCCTGCGGGGCCATACT	1	36	1
AATTGACAGATTTGTGCCATTCCGTGAACGATCGACGCGTCGTG	2	67	1
CCCTGCTTCTTCTTTTTGCTGCCCATTCAGGCGGCTTTTTAGTC	3	41	0
GTTAAGACATTCTGTTCAGCACAATAGCAGGTGGAAAACGCCCT	3	160	0
TTATAGTGAATCCGCTTATTCTCAGGGCGGGGCGAAATTCCCCA	4	45	1
AAATTCCCCACCGGCGGTAAATCAACTCAGTTGAAAGCCCGCGA	4	79	1
TGCTGTCCTTTGAGTTCGCACCCAAAGCGCTCGCGGGCTTTCAA	4	109	0
GACAGCAGATCCGGTGTAATTCCGGGGCCGACGGTTAGAGTCCG	4	146	1
GCCAAAATAACGTGAGCGGGTCCATGCCCGACAGAATCGTTACT	4	200	0
TCACGTTATTTTGGCTATATGCCGCCACTCCTAAGACTGCCCTG	4	229	1
          *  ***     **    * *  **
MAP Score: 4.74578

Motif 9
TTTGTTGTATCGTCAGTTCAGGGTAAAATAGATTTC	0	38	1
      ACGGCGTCCTGACCAGGTGGTTAACGGAAA	0	70	0
     TCTCCCGGCTCGAAAGGGAAGCAGCGCACGA	1	5	1
TCGAGTATGGCCCCGCAGGGGGGCGGATTTTAGCAT	1	47	0
TAACTGAAAACGCCAGTTCCAGGAAAAATTGACAGA	2	41	1
ACGATCGACGCGTCGTGATTAGGTGAACCCCTTCTC	2	94	1
GACTAAAAAGCCGCCTGAATGGGCAGCAAAAAGAAG	3	41	1
GCCATTCTTACCCCTTCACTGGTAAGGGCGTTTTCC	3	136	1
AGTGAATCCGCTTATTCTCAGGGCGGGGCGAAATTC	4	49	1
GGGCGAAATTCCCCACCGGCGGTAAATCAACTCAGT	4	74	1
          **** *    *** **
MAP Score: 3.9508

Motif 10
GTCAGTTCAGGGTAAAATAGATTTCCGTTAAC	0	49	1
GAAATATTATGCTAAAATCCGCCCCCCTGCGG	1	39	1
GCCAGTTCCAGGAAAAATTGACAGATTTGTGC	2	52	1
TTCTCGTTATGGCAAAATAAGCCAATACAGAA	2	125	1
AGAAGAAGCAGGGGAAATTCAGTCTATTGTAG	3	72	1
ATTCTCCAGTGAAAAAATAGCCATTCTTACCC	3	117	1
CTCAGGGCGGGGCGAAATTCCCCACCGGCGGT	4	65	1
CAGCAGATCCGGTGTAATTCCGGGGCCGACGG	4	148	1
GCGGCATATAGCCAAAATAACGTGAGCGGGTC	4	222	0
          GGTAAAAAAACCTCACTAAAAT	4	288	0
          ** ***** ***
MAP Score: 3.7486

Motif 11
TTTGTTGTATCGTCAGTTCAGGGTAAAATAGATTTC	0	38	1
CGCTGCTTCCCTTTCGAGCCGGGAGA          	1	0	0
CTAAAATCCGCCCCCCTGCGGGGCCATACTCGAACC	1	50	1
TAACTGAAAACGCCAGTTCCAGGAAAAATTGACAGA	2	41	1
AATACAGAACCAGCATTATCTGGAGAATTTC     	2	148	1
CTTCTTTTTGCTGCCCATTCAGGCGGCTTTTTAGTC	3	41	0
AAAACGCCCTTACCAGTGAAGGGGTAAGAATGGCTA	3	134	0
TTCTGTTCAGCACAATAGCAGGTGGAAAACGCCCTT	3	159	0
ATCCGCTTATTCTCAGGGCGGGGCGAAATTCCCCAC	4	54	1
GGGCGAAATTCCCCACCGGCGGTAAATCAACTCAGT	4	74	1
ACTCAAAGGACAGCAGATCCGGTGTAATTCCGGGGC	4	138	1
AAATTATGGTTACCAGAATCAGGGCAGTCTTAGGAG	4	256	0
          * ****   ****  *
MAP Score: 1.92982