AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_fusions001_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241423
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	ytgA	300	Solute Protein Binding Family
#1	glnP	206	ABC Amino Acid Transporter Permease
#2	oppB_1	158	Oligopeptide Permease
#3	oppC_1	31	Oligopeptide Permease
#4	accA	132	AcCoA Carboxylase/Transferase Alpha
#5	CT684	300	ABC Transporter
#6	dppD	160	ABC Transport ATPase

Motif 1
CGAGTTTTTATTTTTTTTCGAAACAGAAGTCGT	1	71	1
CTGTCTTTCTTTTTTTTTCAAGAAGGTGTTCGA	5	154	1
TAGGAAAGGCTTTTTTTATAAGAACCTTTCGTT	1	133	1
ATTCGAGATATTTTTTTCGAACACCTTCTTGAA	5	170	0
AAATTTTTTGTTTTTTTCTAAGATTTTTCACGC	6	101	1
TTTGTTTTGCCTTTTTTGAGACAGAGGAGATAA	5	215	1
TAAAATAACTCTTTTTTATAAGAAGGGAGCGTG	4	104	1
          TTTCTTTTTAAGAGAAATTAAAA	4	0	1
AAGCGAGGTTCTTTTTTTGGAGGGGGAGCTCCT	0	116	1
       GAGTTTGTTTTAGAAATCCTTTATTA	3	15	0
AAAATTCCATTTTTTTTACGATTCGTAGCCAAC	5	50	1
CTTTTTTAATTGTCTTTGAGAAAAATGCTCCCA	6	16	1
CTGTTAAAAGTATCTTTGCGATAAGCGAGGTTC	0	94	1
TAATTAAAATCTTTTATCGAAAAAATTTTATAC	1	102	0
AGCCAACAAGTTTTTTTCTTAAGGGCTGTTTGA	5	76	1
AAAAATGGAATTTTTCTACAACACAAACAAATA	5	31	0
          *******  ** *
MAP Score: 18.9967

Motif 2
TCCCCCTCCAAAAAAAGAACCTCGCTTATCGC	0	111	0
TGTATCCTTTAAAATAGAGTTTTTCTTATGAT	0	160	1
AATTTTTTCGATAAAAGATTTTAATTAGGAAA	1	108	1
GATTTTAATTAGGAAAGGCTTTTTTTATAAGA	1	124	1
ACTATATTGAACGAAAGGTTCTTATAAAAAAA	1	143	0
CTCCGTGCGTAGAAAAGATTCTCTCTTTAAAA	2	22	1
AGTTGAAAACATAAAAGGCCTTTGCCAAGAGT	2	90	0
AATACAATATACAAAGGAATCTACT       	2	143	1
    TAATTTAATAAAGGATTTCTAAAACAAA	3	6	1
CCCTTCTTATAAAAAAGAGTTATTTTAATACA	4	99	0
AATCGTAAAAAAAATGGAATTTTTCTACAACA	5	41	0
ACAGCCCTTAAGAAAAAAACTTGTTGGCTACG	5	73	0
GGAGCTCGTGAGAAAAGAGCCTATTATCTCCT	5	239	0
AAAGACAATTAAAAAAGGCTTAT         	6	1	0
TTAGAAAAAAACAAAAAATTTTGGTTCTTAGT	6	90	0
          * ****** ***
MAP Score: 17.452

Motif 3
GTTGTTAAAATTATTTAGAATTGTCTCTTCGAGATGAGAAACGCGCT	0	13	1
TGTCTTTCTTTTTTTTTCAAGAAGGTGTTCGAAAAAAATATCTCGAA	5	155	1
AGGAAAGGCTTTTTTTATAAGAACCTTTCGTTCAATATAGTTACATA	1	134	1
      GAGTTTGTTTTAGAAATCCTTTATTAAATTA          	3	0	0
GCCAACAAGTTTTTTTCTTAAGGGCTGTTTGACAGTCCTTTCCTTGG	5	77	1
TGATTATTGTTTGTATTAAAATAACTCTTTTTTATAAGAAGGGAGCG	4	88	1
AAGGCCTTTTATGTTTTCAACTTGTTATCTGTGATTAGATCGCAATA	2	100	1
GAGGCTTGTATCCTTTAAAATAGAGTTTTTCTTATGATCCCATGTGG	0	154	1
CGTATAAAATTTTTTCGATAAAAGATTTTAATTAGGAAAGGCTTTTT	1	101	1
AGTTTTTATTTTTTTTCGAAACAGAAGTCGTATAAAATTTTTTCGAT	1	73	1
GATTTTTTGATTTTTTATTTGTTTGTGTTGTAGAAAAATTCCATTTT	5	16	1
AAATTTTTTGTTTTTTTCTAAGATTTTTCACGCTCGAGGTCCCCTTC	6	101	1
GAAGGAGGTATATTTTGGGAGCATTTTTCTCAAAGACAATTAAAAAA	6	17	0
AACCAACTATTTGATTATAATGACCTTTGTTTCACGCAAACAATTTT	4	29	0
ATCCTGTCATTAGTATCACAAGAAATGTATGTAACTATATTGAACGA	1	161	0
GAAAAATTCCATTTTTTTTACGATTCGTAGCCAACAAGTTTTTTTCT	5	48	1
CTTCATATATATATTTGCAATCTAGAATGTACTAAGAACCAAAATTT	6	60	1
GGGGATCGTATACTTTTTCAAAGTATGTCCCCGTATCGATTATCTGG	0	255	1
          ** ***   *     * *     *  *
MAP Score: 16.2015

Motif 4
TGTACACGAGTTTTTATTTTTTTTCGAAACAGAAGTC	1	65	1
  ATAAGCCTTTTTTAATTGTCTTTGAGAAAAATGCT	6	8	1
AAATAGTTGGTTTTTGGTTGTTTTTGATTATTGTTTG	4	64	1
AAAATAACTCTTTTTTATAAGAAGGGAGCGTGCTACG	4	105	1
ATTTTTTGATTTTTTATTTGTTTGTGTTGTAGAAAAA	5	17	1
AAAAATTCCATTTTTTTTACGATTCGTAGCCAACAAG	5	49	1
CCAACAAGTTTTTTTCTTAAGGGCTGTTTGACAGTCC	5	78	1
AAAGAGAGAATCTTTTCTACGCACGGAGTAAAAACAT	2	13	0
AGAACCAAAATTTTTTGTTTTTTTCTAAGATTTTTCA	6	94	1
AACGCGCTAGATTTTCCTTTTGGTTGAGGATATAAAT	0	52	1
TAAGCGAGGTTCTTTTTTTGGAGGGGGAGCTCCTTAC	0	115	1
TCAGGATTTGTTTTGCCTTTTTTGAGACAGAGGAGAT	5	209	1
TAGGCTGTCTTTCTTTTTTTTTCAAGAAGGTGTTCGA	5	150	1
TAAAATAGAGTTTTTCTTATGATCCCATGTGGCGATA	0	169	1
TCGATAAAAGATTTTAATTAGGAAAGGCTTTTTTTAT	1	115	1
AGGAAAGGCTTTTTTTATAAGAACCTTTCGTTCAATA	1	134	1
AAAGATTCTCTCTTTAAAATGCGGAGAGGTCTTGTCT	2	35	1
          *****  ** *    **
MAP Score: 12.9177

Motif 5
TGTTAAAATTATTTAGAATTGTCTCTTCGAGATGAGAAACGC	0	15	1
GAAACGCGCTAGATTTTCCTTTTGGTTGAGGATATAAATTCA	0	50	1
  ATCATCCTAATAAACTATCTTGTAAGCCGACAATACTTTT	1	8	1
TAAAATGTACACGAGTTTTTATTTTTTTTCGAAACAGAAGTC	1	60	1
CAGAAGTCGTATAAAATTTTTTCGATAAAAGATTTTAATTAG	1	94	1
GATTTTAATTAGGAAAGGCTTTTTTTATAAGAACCTTTCGTT	1	124	1
CTCCGTGCGTAGAAAAGATTCTCTCTTTAAAATGCGGAGAGG	2	22	1
AAGAGTGATAATTTAACACTCTCTAGACAAGACCTCTCCGCA	2	54	0
    TAATTTAATAAAGGATTTCTAAAACAAACTC       	3	6	1
CACGCAAACAATTTTAATTTCTCTTAAAAAGAAA        	4	2	0
AAAACAACCAAAAACCAACTATTTGATTATAATGACCTTTGT	4	46	0
CCTTCTTATAAAAAAGAGTTATTTTAATACAAACAATAATCA	4	88	0
TGTGTTGTAGAAAAATTCCATTTTTTTTACGATTCGTAGCCA	5	39	1
AGCCCTTAAGAAAAAAACTTGTTGGCTACGAATCGTAAAAAA	5	61	0
CCTGAACTGCAATTCGAGATATTTTTTTCGAACACCTTCTTG	5	172	0
GACAGAGGAGATAATAGGCTCTTTTCTCACGAGCTCCACTCC	5	234	1
TTTCATCAGGATGCCACTCTATTTGGAGTGGAGCTCGTGAGA	5	258	0
ACTAAGAACCAAAATTTTTTGTTTTTTTCTAAGATTTTTCAC	6	90	1
  AGCTATGTATCTCCTACTATTTGAAGGGGACCTCGAGCGT	6	130	0
          *  *    ** ***  *   **
MAP Score: 12.1083

Motif 6
GTACACGAGTTTTTATTTTTTTTCGAAACAGA	1	66	1
CTAGGCTGTCTTTCTTTTTTTTTCAAGAAGGT	5	149	1
AACCAAAATTTTTTGTTTTTTTCTAAGATTTT	6	96	1
ATAGTTGGTTTTTGGTTGTTTTTGATTATTGT	4	66	1
ATAAGCCTTTTTTAATTGTCTTTGAGAAAAAT	6	10	1
TGATTTTTTATTTGTTTGTGTTGTAGAAAAAT	5	23	1
CAGGATTTGTTTTGCCTTTTTTGAGACAGAGG	5	210	1
CTAGCGATTTTTTGATTTTTTATTTGTTTGTG	5	11	1
TGTAGAAAAATTCCATTTTTTTTACGATTCGT	5	44	1
CGCGCTAGATTTTCCTTTTGGTTGAGGATATA	0	54	1
          ***  *******
MAP Score: 10.4361

Motif 7
TTTAGAATTGTCTCTTCGAGATGAGAAACGCGC	0	26	1
GCTAGATTTTCCTTTTGGTTGAGGATATAAATT	0	57	1
GTTAAAAGTATCTTTGCGATAAGCGAGGTTCTT	0	96	1
TAAGCGAGGTTCTTTTTTTGGAGGGGGAGCTCC	0	115	1
GGATCGTATACTTTTTCAAAGTATGTCCCCGTA	0	257	1
AGTTTTTATTTTTTTTCGAAACAGAAGTCGTAT	1	73	1
TCGTATAAAATTTTTTCGATAAAAGATTTTAAT	1	100	1
ATAAAAAAAGCCTTTCCTAATTAAAATCTTTTA	1	119	0
TTAGGAAAGGCTTTTTTTATAAGAACCTTTCGT	1	132	1
AAAGAGAGAATCTTTTCTACGCACGGAGTAAAA	2	17	0
GAAAAGATTCTCTCTTTAAAATGCGGAGAGGTC	2	33	1
ACATAAAAGGCCTTTGCCAAGAGTGATAATTTA	2	81	0
         TTTCTTTTTAAGAGAAATTAAAAT	4	1	1
ATTATAATGACCTTTGTTTCACGCAAACAATTT	4	30	0
TTAAAATAACTCTTTTTTATAAGAAGGGAGCGT	4	103	1
AGCCAACAAGTTTTTTTCTTAAGGGCTGTTTGA	5	76	1
TGTTTGACAGTCCTTTCCTTGGGTCTAGGGAGA	5	102	1
GCTGTCTTTCTTTTTTTTTCAAGAAGGTGTTCG	5	153	1
CAATTCGAGATATTTTTTTCGAACACCTTCTTG	5	172	0
TTTGTTTTGCCTTTTTTGAGACAGAGGAGATAA	5	215	1
AGATAATAGGCTCTTTTCTCACGAGCTCCACTC	5	242	1
   GATCCTCCTCTTTCATCAGGATGCCACTCT	5	280	0
     ATAAGCCTTTTTTAATTGTCTTTGAGAA	6	5	1
ATTTTGGGAGCATTTTTCTCAAAGACAATTAAA	6	20	0
AAATTTTTTGTTTTTTTCTAAGATTTTTCACGC	6	101	1
CGCTCGAGGTCCCCTTCAAATAGTAGGAGATAC	6	131	1
          ******* * * *
MAP Score: 10.2164