AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID005_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943390924
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	cof	87	orf, hypothetical protein
#1	ybaO	65	putative LRP-like transcriptional regulator
#2	mdlA	29	ATP-binding component of a transport system
#3	glnK	180	nitrogen regulatory protein P-II 2
#4	amtB	29	probable ammonium transporter
#5	glnB	60	regulatory protein P-II for glutamine synthetase
#6	yfhG	164	putative alpha helix protein
#7	yfhK	300	putative 2-component sensor protein

Motif 1
CGAGATCCCTTCCAGCACCGGGCAATTGCCCGG	1	10	1
TGCAAAAATGTAACGCACTGTGCACTGTCATAG	3	33	1
GTTTTTCATTTCTGGCACACCGCTTGCAATACC	3	110	1
        TCTCTGGCACACAGCAACAGGAACG	4	2	1
TATTTGTCAGTTCGGCCCCGGGCAGTGCTCGAA	6	39	1
TCTGCAACAATTACGCCCACTGGGATAGGCTTT	6	128	1
TGAATGTAAATCAGCCACTGTGTCG        	7	2	0
CCGACTTATGTCAGCCCCTTCGGGACGTGCTAC	7	144	1
AAGTTGGACGGCAGGCACCTTGTTGTGCGTCAT	7	188	0
TAACTCGACGTTTCGCCCGATGGTTGATATAGC	7	235	0
AAACGTCGAGTTAGGCACCGCCTTATTCCATAA	7	255	1
          ********   **
MAP Score: 9.96393

Motif 2
   CGAGATCCCTTCCAGCACCGGGCAATTGCCCGGTTTTTTT	1	7	1
TTTTATTTGTCAGTTCGGCCCCGGGCAGTGCTCGAAATCTTCA	6	36	1
TTTCTCCGCGCTGTCCATGTCCAGACTGTCTGCAACAATTACG	6	100	1
AACGTATAATCAGTACGTTACCAAACTATTTTCTTTATTGGCA	7	66	1
TGGAATAAGGCGGTGCCTAACTCGACGTTTCGCCCGATGGTTG	7	242	0
CGCCTTATTCCATAACAAAGCCGGGTAATTCCCGGCT      	7	273	1
          * ** *    ** * *  *   *
MAP Score: 8.13336

Motif 3
AGATCCCTTCCAGCACCGGGCAATTGCCCGGTTTTTTTTGCG	1	12	1
     ATATCCAGAATCAGGTCAGGACACAACGC        	2	5	1
TGACAGTGCACAGTGCGTTACATTTTTGCACCAACGATGAAA	3	21	0
ATTTCTGGCACACCGCTTGCAATACCTTCTTCGTGTAGCAGA	3	117	1
CCCCTCCGGTCAGAATTCGGTAATGGTTCTGCTACACGAAGA	3	144	0
CGGCCCCGGGCAGTGCTCGAAATCTTCACGTACGATATGTAC	6	51	1
AAGCCTATCCCAGTGGGCGTAATTGTTGCAGACAGTCTGGAC	6	118	0
     CGACACAGTGGCTGATTTACATTCAAACAGCGGAGGA	7	5	1
TACATTCAAACAGCGGAGGAGACATAAACCCCTCAAAGCAAC	7	27	1
TAATAGTAACCAGTGGCTCATTCACCGACTTATGTCAGCCCC	7	120	1
CGACTTATGTCAGCCCCTTCGGGACGTGCTACATAAAATACG	7	145	1
ACGCTGATATCAGAAGTTGGACGGCAGGCACCTTGTTGTGCG	7	192	0
CTTCTGATATCAGCGTAGCTATATCAACCATCGGGCGAAACG	7	218	1
          ******  *     *   *  *
MAP Score: 7.98744

Motif 4
AGATCCCTTCCAGCACCGGGCAATTGCCCGGTTTTTTTT	1	12	1
TTCATTTCTGGCACACCGCTTGCAATACCTTCTTCGTGT	3	114	1
      AGATCCCCTCCGGTCAGAATTCGGTAATGGTTC	3	157	0
TTTGTCAGTTCGGCCCCGGGCAGTGCTCGAAATCTTCAC	6	41	1
TACGATATGTACGCTCCGGTTTCTCCGCGCTGTCCATGT	6	81	1
GGGTTTATGTCTCCTCCGCTGTTTGAATGTAAATCAGCC	7	19	0
AGGGGCTGACATAAGTCGGTGAATGAGCCACTGGTTACT	7	124	0
CTTATGTCAGCCCCTTCGGGACGTGCTACATAAAATACG	7	148	1
TAGCTATATCAACCATCGGGCGAAACGTCGAGTTAGGCA	7	233	1
TATTCCATAACAAAGCCGGGTAATTCCCGGCT       	7	278	1
          *  * *****   *   **
MAP Score: 7.97966

Motif 5
    CGAGATCCCTTCCAGCACCGGGCAATTGCCCG	1	6	1
ACAAATTCAACGCAAAAAAAACCGGGCAATTGCCCG	1	28	0
GAACCATTACCGAATTCTGACCGGAGGGGATCT   	3	157	1
GTGAAGATTTCGAGCACTGCCCGGGGCCGAACTGAC	6	44	0
ACAGTCTGGACATGGACAGCGCGGAGAAACCGGAGC	6	93	0
GGCTGATTTACATTCAAACAGCGGAGGAGACATAAA	7	19	1
CCGCCTTATTCCATAACAAAGCCGGGTAATTCCCGG	7	272	1
          *     **** *****
MAP Score: 5.16601

Motif 6
TTGTGTCCTGACCTGATTCTGGATAT     	2	5	0
CGCTTGCAATACCTTCTTCGTGTAGCAGAAC	3	130	1
CAGAACCATTACCGAATTCTGACCGGAGGGG	3	155	1
TGGCTCATTCACCGACTTATGTCAGCCCCTT	7	133	1
GTGCCTGCCGTCCAACTTCTGATATCAGCGT	7	203	1
CGAGTTAGGCACCGCCTTATTCCATAACAAA	7	261	1
          **** ******
MAP Score: 2.37875

Motif 7
GTTTGAATGTAAATCAGCCACTGTGTCG   	7	7	0
ATAAGTCGGTGAATGAGCCACTGGTTACTAT	7	122	0
TCACCGACTTATGTCAGCCCCTTCGGGACGT	7	141	1
CATAAAATACGAATGACGCACAACAAGGTGC	7	176	1
GCGAAACGTCGAGTTAGGCACCGCCTTATTC	7	252	1
          **** ******
MAP Score: 0.128094