AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_fusions001_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241446
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	ytgA	300	Solute Protein Binding Family
#1	glnP	206	ABC Amino Acid Transporter Permease
#2	CT196	223	hypothetical protein
#3	gcp_1	75	O-Sialoglycoprotein Endopeptidase
#4	oppB_1	158	Oligopeptide Permease
#5	oppC_1	31	Oligopeptide Permease
#6	accA	132	AcCoA Carboxylase/Transferase Alpha
#7	CT266	117	hypothetical protein
#8	himD	219	Integration Host Factor Alpha
#9	murE	300	UDP-N-acetylmuramoylalanylglutamyl DAP Ligase
#10	CT684	300	ABC Transporter
#11	dppD	160	ABC Transport ATPase

Motif 1
AGGAAAGGCTTTTTTTATAAGAACCTTTCGTT	1	134	1
AAAATAACTCTTTTTTATAAGAAGGGAGCGTG	6	105	1
TGTCTTTCTTTTTTTTTCAAGAAGGTGTTCGA	10	155	1
AATTTTTTGTTTTTTTCTAAGATTTTTCACGC	11	102	1
AAGAAATGTTTTGTTTGTGAGATGTAATTATG	9	101	0
TTCGAGATATTTTTTTCGAACACCTTCTTGAA	10	170	0
AAGAGTTACTTTTTTTGTGAAAGAGTAAAAAG	9	143	1
GAGTTTTTATTTTTTTTCGAAACAGAAGTCGT	1	72	1
TTGTTTTGCCTTTTTTGAGACAGAGGAGATAA	10	216	1
TTGGGAGCATTTTTCTCAAAGACAATTAAAAA	11	18	0
AGCGAGGTTCTTTTTTTGGAGGGGGAGCTCCT	0	117	1
AAAAATTCCATTTTTTTTACGATTCGTAGCCA	10	49	1
         TTTCTTTTTAAGAGAAATTAAAA	6	1	1
      GAGTTTGTTTTAGAAATCCTTTATTA	5	15	0
GAAATTAAAATTGTTTGCGTGAAACAAAGGTC	6	23	1
TCGTATAAAATTTTTTCGATAAAAGATTTTAA	1	100	1
TAAAATAGAGTTTTTCTTATGATCCCATGTGG	0	169	1
AAAATGGAATTTTTCTACAACACAAACAAATA	10	31	0
CCAACAAGTTTTTTTCTTAAGGGCTGTTTGAC	10	78	1
CTATTTCATTTCTTTTGCAAAAACTCTCTACT	2	173	1
ACTTTTTTTATCTTTTCCATGAACGCACAAAA	8	103	0
          ******  ****
MAP Score: 20.8994

Motif 2
TCCCCCTCCAAAAAAAGAACCTCGCTTATCGCAA	0	109	0
AAGGTGTTCGAAAAAAATATCTCGAATTGCAGTT	10	176	1
CTCTTTCACAAAAAAAGTAACTCTTATATGGAGC	9	134	0
GTCCAATGGCAAAAAATAATCTTGAGGAAATTTA	7	78	0
CCGTGCGTAGAAAAGATTCTCTCTTTAAAATGCG	4	24	1
GGTTCTTATAAAAAAAGCCTTTCCTAATTAAAAT	1	125	0
TGAAAGAGTAAAAAGACGAGTTCTCTTGTCTTTG	9	160	1
CAGAAGTCGTATAAAATTTTTTCGATAAAAGATT	1	94	1
TTTACTAATTAAAAAAACCGTTTTATTTCTAAGT	2	84	1
GGCTTTTTTTATAAGAACCTTTCGTTCAATATAG	1	140	1
CTTCTTATAAAAAAGAGTTATTTTAATACAAACA	6	95	0
ACATCTCACAAACAAAACATTTCTTTGCTCCATA	9	108	1
GTTTCGAAAAAAAATAAAAACTCGTGTACATTTT	1	61	0
AGTTGAAAACATAAAAGGCCTTTGCCAAGAGTGA	4	88	0
  ATCATCCTAATAAACTATCTTGTAAGCCGACA	1	8	1
    TAATTTAATAAAGGATTTCTAAAACAAACT	5	6	1
GCCCTTAAGAAAAAAACTTGTTGGCTACGAATCG	10	68	0
CTTAGAAAAAAACAAAAAATTTTGGTTCTTAGTA	11	89	0
AACTTGGGACAAAAGAATGGCTTCAACTTTGTAA	2	40	0
ACATGGGATCATAAGAAAAACTCTATTTTAAAGG	0	165	0
AATAATAAAGAAAAGAGCAATTTCATAATTACAT	9	78	1
TTTAAGAGAAATTAAAATTGTTTGCGTGAAACAA	6	16	1
          ******    ****
MAP Score: 16.7019

Motif 3
AAATAGAGTTTTTCTTATGATCCCATGTGG	0	171	1
GAGTTTTTATTTTTTTTCGAAACAGAAGTC	1	72	1
GAAAGGCTTTTTTTATAAGAACCTTTCGTT	1	136	1
GTTACATACATTTCTTGTGATACTAATGAC	1	173	1
ATAAAACGGTTTTTTTAATTAGTAAAATCT	2	80	0
GCGGTTGATATTTCTTGATTAGTCGACTTA	2	113	0
      CGCCTTGCTTGATTAACAATCTCA	3	4	1
TGTTTCCCTCTTTTTTAAGTGTTCGCT   	3	58	1
GGCAAAGGCCTTTTATGTTTTCAACTTGTT	4	96	1
      GAGTTTGTTTTAGAAATCCTTTAT	5	17	0
          TTTCTTTTTAAGAGAAATTA	6	0	1
GAAATTAAAATTGTTTGCGTGAAACAAAGG	6	23	1
TGGTTTTTGGTTGTTTTTGATTATTGTTTG	6	71	1
TTTTTGATTATTGTTTGTATTAAAATAACT	6	84	1
TTTCCCGGCTTTGCTTTCGATCGTAGAGTC	7	21	1
CTCAAGATTATTTTTTGCCATTGGACGTCT	7	86	1
AAATTGCTCTTTTCTTTATTATTAGTTTCC	9	71	0
AAGAAATGTTTTGTTTGTGAGATGTAATTA	9	103	0
AAGAGTTACTTTTTTTGTGAAAGAGTAAAA	9	143	1
  TCTAGCGATTTTTTGATTTTTTATTTGT	10	8	1
GATTTTTTATTTGTTTGTGTTGTAGAAAAA	10	24	1
AAATTCCATTTTTTTTACGATTCGTAGCCA	10	51	1
AGCCAACAAGTTTTTTTCTTAAGGGCTGTT	10	76	1
CTAGGCTGTCTTTCTTTTTTTTTCAAGAAG	10	149	1
ATTCGAGATATTTTTTTCGAACACCTTCTT	10	173	0
TTGTTTTGCCTTTTTTGAGACAGAGGAGAT	10	216	1
   ATAAGCCTTTTTTAATTGTCTTTGAGA	11	7	1
AGAACCAAAATTTTTTGTTTTTTTCTAAGA	11	94	1
          **********
MAP Score: 16.6181

Motif 4
ACGCGCTAGATTTTCCTTTTGGTTGAGGATA	0	53	1
GTACACGAGTTTTTATTTTTTTTCGAAACAG	1	66	1
CTTCTAAAAATTTTACTTTTACAAAGTTGAA	2	22	1
TAATGCTATTTCATTTCTTTTGCAAAAACTC	2	168	1
GGCAAAGGCCTTTTATGTTTTCAACTTGTTA	4	96	1
       TCTTCTTCCCTTTTCCCGGCTTTG	7	3	1
CAAGATTATTTTTTGCCATTGGACGTCTTTT	7	88	1
TCAAGACTTTTTTTATCTTTTCCATGAACGC	8	109	0
ATGAAATTGCTCTTTTCTTTATTATTAGTTT	9	73	0
AGAACTCGTCTTTTTACTCTTTCACAAAAAA	9	153	0
AGACGAGTTCTCTTGTCTTTGCTCTTTCTCT	9	173	1
TCTAGCGATTTTTTGATTTTTTATTTGTTTG	10	10	1
CCCTAGGCTGTCTTTCTTTTTTTTTCAAGAA	10	147	1
TCAGGATTTGTTTTGCCTTTTTTGAGACAGA	10	209	1
AACCAAAATTTTTTGTTTTTTTCTAAGATTT	11	96	1
          **** ******
MAP Score: 6.73573

Motif 5
TACACGAGTTTTTATTTTTTTTCGAAACAGAA	1	67	1
ATAATGCTATTTCATTTCTTTTGCAAAAACTC	2	167	1
CCAAAATGTTTCCCTCTTTTTTAAGTGTTCGC	3	52	1
TAGTTGGTTTTTGGTTGTTTTTGATTATTGTT	6	67	1
TATTAAAATAACTCTTTTTTATAAGAAGGGAG	6	101	1
CATATAAGAGTTACTTTTTTTGTGAAAGAGTA	9	138	1
TAGCGATTTTTTGATTTTTTATTTGTTTGTGT	10	12	1
GTAGAAAAATTCCATTTTTTTTACGATTCGTA	10	45	1
CCCTAGGCTGTCTTTCTTTTTTTTTCAAGAAG	10	147	1
TAAGCCTTTTTTAATTGTCTTTGAGAAAAATG	11	11	1
AGAACCAAAATTTTTTGTTTTTTTCTAAGATT	11	94	1
          **  ********
MAP Score: 1.1425