AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_profile005_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243468
 numcols =     	10
 undersample = 	1
 oversample = 	1

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

Motif 1
        AACTATTTTTTAAGAATACAAA	4	96	0
TGTCGAAATTCTTTTTTTTAGCGCTCCAAA	5	252	1
ATGCTATCCCCTATTTTTTATGCACCTATT	5	77	1
TTTTATGCACCTATTTTTTATCAACTCCCC	5	92	1
CCAAAAAACCCTTTTTCTTAACCTCTCAAT	5	120	1
AAATTTTCCTCTCTTTTTTTCTTTTTTTTG	5	191	1
CTCTTTTTTTCTTTTTTTTGCTCATCCTAC	5	201	1
ATAAGAAAAACTCTATTTTAAAGGATACAA	1	159	0
  TGTACACTCTCCTTCTTATCGTAGAGGG	3	8	1
CGAAAGAAAGCTACATCTTATGCTATCCCC	5	58	1
          **********
MAP Score: 15.3983

Motif 2
CATGGAGAAACTTCCCTTTAAAAATTGT  	0	8	0
TCCATGGAGACCTTCCTTTAAATTGATCTA	0	32	1
GGCCGAATCTCTTTCTCCTAAAGGTTTTGG	0	84	0
CAGGAGGCTTGTATCCTTTAAAATAGAGTT	1	151	1
TTAAAATAGAGTTTTTCTTATGATCCCATG	1	168	1
AAAAAGTATACGATCCCCTAAGGACAAAAA	1	243	0
 AAGAACCTCGTATTCTCTACATTGCC   	2	7	0
        AACTATTTTTTAAGAATACAAA	4	96	0
ACGTAAGAGGCCTTCCTTCAACCCTCGTTC	5	29	1
ATAAGATGTAGCTTTCTTTCGAACGAGGGT	5	49	0
ACATCTTATGCTATCCCCTATTTTTTATGC	5	70	1
TTTTATGCACCTATTTTTTATCAACTCCCC	5	92	1
CCAAAAAACCCTTTTTCTTAACCTCTCAAT	5	120	1
CCCTCACACACTATCCTTAACACTTTTTAT	5	155	1
CTCATCCTACCCTTCCTCTCTTCGATTTTT	5	221	1
TGTCGAAATTCTTTTTTTTAGCGCTCCAAA	5	252	1
          **********
MAP Score: 9.25009

Motif 3
AACAGAATGAATTTATATCCTCAACCAAAAGG	1	67	0
AAATAGAGTTTTTCTTATGATCCCATGTGGCG	1	171	1
GTGGTCAAAAATTTTAACCCTCTACGATAAGA	3	23	0
GAGGGTTAAAATTTTTGACCACAAGATTGAAG	3	33	1
CTATCCCCTATTTTTTATGCACCTATTTTTTA	5	80	1
TATGCACCTATTTTTTATCAACTCCCCAAAAA	5	95	1
AAAAACCCTTTTTCTTAACCTCTCAATTTATC	5	123	1
TAACCTCTCAATTTATCCCCTCACACACTATC	5	138	1
TCTTTTTTTCTTTTTTTTGCTCATCCTACCCT	5	202	1
TCGAAATTCTTTTTTTTAGCGCTCCAAACAAG	5	254	1
          ******  ****
MAP Score: 9.0821

Motif 4
ACAGAATGAATTTATATCCTCAACCAAAAGGAAAATC	1	61	0
TAAAATAGAGTTTTTCTTATGATCCCATGTGGCGATA	1	169	1
       AACTATTTTTTAAGAATACAAAATCTTGAG	4	88	0
TGCTATCCCCTATTTTTTATGCACCTATTTTTTATCA	5	78	1
ATGCACCTATTTTTTATCAACTCCCCAAAAAACCCTT	5	96	1
CAAAAAACCCTTTTTCTTAACCTCTCAATTTATCCCC	5	121	1
CTTTTTTTCTTTTTTTTGCTCATCCTACCCTTCCTCT	5	203	1
TCGAAATTCTTTTTTTTAGCGCTCCAAACAAGCTTAC	5	254	1
          ***** *   *  ** *
MAP Score: 7.43934

Motif 5
TTATACTTCCTCAGCCCCCCAAAACCTTTAGGAG	0	66	1
CAGAATGAATTTATATCCTCAACCAAAAGGAAAA	1	63	0
CCTGTAAGGAGCTCCCCCTCCAAAAAAAGAACCT	1	121	0
TGTATGTGCGTCATCTCTACAGAAGGAA      	3	65	1
TTTAAGATTATTTCCGCCTATAAAAACCCGATTG	4	51	1
TATCGCGCCCTCTCATCCACGTAAGAGGCCTTCC	5	11	1
CTATTTTTTATCAACTCCCCAAAAAACCCTTTTT	5	102	1
AAACCCTTTTTCTTAACCTCTCAATTTATCCCCT	5	125	1
ACCTCTCAATTTATCCCCTCACACACTATCCTTA	5	140	1
TTTTCTTTTTTTTGCTCATCCTACCCTTCCTCTC	5	207	1
ATTCTTTTTTTTAGCGCTCCAAACAAGCTTACAT	5	259	1
          *** * ****  **
MAP Score: 3.37294

Motif 6
TCAGCCCCCCAAAACCTTTAGGAGAAAGAGA	0	76	1
GCCAATTTCAAAAATTGTTTGTAGGACACCT	0	126	1
TTAGTTGTTAAAATTATTTAGAATTGTCTCT	1	10	1
AACCAAAAGGAAAATCTAGCGCGTTTCTCAT	1	46	0
ATCATAAGAAAAACTCTATTTTAAAGGATAC	1	161	0
AAATAATCTTAAAGTCTATAGTACTTTCGAG	4	33	0
CCGCCTATAAAAACCCGATTGACTCTCAAGA	4	64	1
TTAAGAATACAAAATCTTGAGAGTCAATCGG	4	78	0
ACTCCCCAAAAAACCCTTTTTCTTAACCTCT	5	115	1
AAAAGAGAGGAAAATTTTGTTTTATAAAAAG	5	177	0
TTTTTTGTCGAAATTCTTTTTTTTAGCGCTC	5	247	1
          *** *******
MAP Score: 3.25616

Motif 7
CTCCATGGAGACCTTCCTTTAAATTGATCT	0	31	1
TACCGGCCGAATCTCTTTCTCCTAAAGGTT	0	88	0
AACGCGCTAGATTTTCCTTTTGGTTGAGGA	1	52	1
    TGTACACTCTCCTTCTTATCGTAGAG	3	6	1
CCCCAAAAAACCCTTTTTCTTAACCTCTCA	5	118	1
ATAAAACAAAATTTTCCTCTCTTTTTTTCT	5	183	1
ATTTTCCTCTCTTTTTTTCTTTTTTTTGCT	5	193	1
GCTCATCCTACCCTTCCTCTCTTCGATTTT	5	220	1
CCTCTCTTCGATTTTTTTGTCGAAATTCTT	5	235	1
TTGTCGAAATTCTTTTTTTTAGCGCTCCAA	5	251	1
          **********
MAP Score: 1.05115

Motif 8
CTAAAGGTTTTGGGGGGCTGAGGAAGTATAAG	0	65	0
CCAAAACCTTTAGGAGAAAGAGATTCGGCCGG	0	84	1
GGTTCTTTTTTTGGAGGGGGAGCTCCTTACAG	1	122	1
    GGCAATGTAGAGAATACGAGGTTCTT  	2	6	1
CCTTCTTATCGTAGAGGGTTAAAATTTTTGAC	3	20	1
  TTCCTTCTGTAGAGATGACGCACATACACT	3	63	0
AATCGGGTTTTTATAGGCGGAAATAATCTTAA	4	52	0
CTTACGTGGATGAGAGGGCGCGATAG      	5	4	0
AAAAAATAGGGGATAGCATAAGATGTAGCTTT	5	64	0
GGGGATAAATTGAGAGGTTAAGAAAAAGGGTT	5	126	0
GGATAGTGTGTGAGGGGATAAATTGAGAGGTT	5	139	0
AAGAGAGGAAGGGTAGGATGAGCAAAAAAAAG	5	211	0
GTAAGCTTGTTTGGAGCGCTAAAAAAAAGAAT	5	259	0
          *******  ***
MAP Score: 0.874593