AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_profile005_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243482
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	gcpE	151	hypothetical protein
#1	CT058	79	hypothetical protein
#2	fer	181	Ferredoxin
#3	ytgA	300	Solute Protein Binding Family
#4	yaeM	26	hypothetical protein
#5	araD	83	Ribulose-P Epimerase
#6	rnc	108	Ribonuclease III
#7	alaS	300	Alanyl tRNA Synthetase

Motif 1
ACCGGCCGAATCTCTTTCTCCTAAAGGTTT	0	87	0
  TTACAGTATCTTTCTCTTGTCTAGTATA	2	8	1
TTCCTTAGCTCCTACTTTTTTAAATCGGAG	2	54	1
TCTTAACTAATCTTTTCTTTTTCCTTCTGG	2	155	1
TAAGCGAGGTTCTTTTTTTGGAGGGGGAGC	3	115	1
   TGTACACTCTCCTTCTTATCGTAGAGG	5	7	1
         AACTATTTTTTAAGAATACAA	6	97	0
TATGCTATCCCCTATTTTTTATGCACCTAT	7	76	1
TTTTTATGCACCTATTTTTTATCAACTCCC	7	91	1
CCCAAAAAACCCTTTTTCTTAACCTCTCAA	7	119	1
AAAATTTTCCTCTCTTTTTTTCTTTTTTTT	7	190	1
TCTCTTTTTTTCTTTTTTTTGCTCATCCTA	7	200	1
CTTCCTCTCTTCGATTTTTTTGTCGAAATT	7	232	1
TTGTCGAAATTCTTTTTTTTAGCGCTCCAA	7	251	1
          **********
MAP Score: 16.3406

Motif 2
GGAGAAACTTCCCTTTAAAAATTGT      	0	4	0
CGCTATACTCCGATTTAAAAAAGTAGGAGCT	2	60	0
GGAGCTCCCCCTCCAAAAAAAGAACCTCGCT	3	117	0
CGAGTTTATTCGCCTAAATAAGTGAGT    	6	6	0
AGATTATTTCCGCCTATAAAAACCCGATTGA	6	55	1
AGATTTTGTATTCTTAAAAAATAGTT     	6	92	1
AAAAAATAGGTGCATAAAAAATAGGGGATAG	7	80	0
TTTATCAACTCCCCAAAAAACCCTTTTTCTT	7	108	1
GGGTAGGATGAGCAAAAAAAAGAAAAAAAGA	7	202	0
AAAAGAATTTCGACAAAAAAATCGAAGAGAG	7	236	0
TTGTTTGGAGCGCTAAAAAAAAGAATTTCGA	7	254	0
          *** *******
MAP Score: 7.36961

Motif 3
CCCCCCAAAACCTTTAGGAGAAAGAGATTC	0	80	1
ATTTCAAAAATTGTTTGTAGGACACCTCGT	0	130	1
GGACAACACACCGTTTTGCGCAAGAACGCA	1	22	0
TTTTCTTTTTCCTTCTGGAGTCCT      	2	167	1
GCGAGGTTCTTTTTTTGGAGGGGGAGCTCC	3	118	1
CCCGTATCGATTATCTGGAGGCTCTT    	3	284	1
        TTCCTTCTGTAGAGATGACGCA	5	71	0
TAAGATGTAGCTTTCTTTCGAACGAGGGTT	7	48	0
AGAAAAAGGGTTTTTTGGGGAGTTGATAAA	7	108	0
CTCTTTTTTTCTTTTTTTTGCTCATCCTAC	7	201	1
TCTCTTCGATTTTTTTGTCGAAATTCTTTT	7	237	1
GTCGAAATTCTTTTTTTTAGCGCTCCAAAC	7	253	1
AGATGTAAGCTTGTTTGGAGCGCTAAAAAA	7	265	0
          **********
MAP Score: 7.14196

Motif 4
AAACCTTTAGGAGAAAGAGATTCGGCCGGTACTGT	0	87	1
CAAACAATTTTTGAAATTGGCTGGGACAGTACCGG	0	112	0
ACACCGTTTTGCGCAAGAACGCAGGTGTCCGGAGG	1	10	0
TAAAATTTTTGCCCAAGAGCAAAGGACAACACACC	1	40	0
AGCCTGGTTAGCGCGGTTGCTTTGGGAGCAATAGG	2	92	1
GTTGCTTTGGGAGCAATAGGTCGGGGGTTCGAATC	2	107	1
AAAAGTATCTTTGCGATAAGCGAGGTTCTTTTTTT	3	99	1
TGATCCCATGTGGCGATAGGCCGGGTCTAGCGCCG	3	188	1
AAAAATCGAAGAGAGGAAGGGTAGGATGAGCAAAA	7	216	0
          * **** ***   **
MAP Score: 4.90936

Motif 5
GGACACCTGCGTTCTTGCGCAAAACGGTGT	1	15	1
TTTAAATCGGAGTATAGCGCAGCCTGGTTA	2	72	1
TAGCGCAGCCTGGTTAGCGCGGTTGCTTTG	2	86	1
CCAAAAGGAAAATCTAGCGCGTTTCTCATC	3	45	0
CGCTAGACCCGGCCTATCGCCACATGGGAT	3	190	0
CGATAGGCCGGGTCTAGCGCCGATAGTAGA	3	201	1
GAAATTCTTTTTTTTAGCGCTCCAAACAAG	7	256	1
          **********
MAP Score: 3.23129

Motif 6
CGGCCGAATCTCTTTCTCCTAAAGGTTTTG	0	85	0
  TTACAGTATCTTTCTCTTGTCTAGTATA	2	8	1
CTTCCTTAGCTCCTACTTTTTTAAATCGGA	2	53	1
TTCTTAACTAATCTTTTCTTTTTCCTTCTG	2	154	1
CTTTTCTTTTTCCTTCTGGAGTCCT     	2	166	1
CGCTAGATTTTCCTTTTGGTTGAGGATATA	3	56	1
GGATATAAATTCATTCTGTTAAAAGTATCT	3	79	1
ATAAGCGAGGTTCTTTTTTTGGAGGGGGAG	3	114	1
TAAAATAGAGTTTTTCTTATGATCCCATGT	3	169	1
 TGTACACTCTCCTTCTTATCGTAGAGGGT	5	9	1
         TTCCTTCTGTAGAGATGACGC	5	72	0
AAACAAAATTTTCCTCTCTTTTTTTCTTTT	7	186	1
CTCTCTTTTTTTCTTTTTTTTGCTCATCCT	7	199	1
CATCCTACCCTTCCTCTCTTCGATTTTTTT	7	223	1
CTCTCTTCGATTTTTTTGTCGAAATTCTTT	7	236	1
TTTGTCGAAATTCTTTTTTTTAGCGCTCCA	7	250	1
          **********
MAP Score: 3.22595