AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_fusions003_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236878
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	CPn0456	300	hypothetical protein
#1	CPn0461	300	hypothetical protein
#2	CPn0464	25	hypothetical protein
#3	CPn0465	300	hypothetical protein

Motif 1
ACGTTATCGATTCTTAGGGGAAATAGGTTCTGACAATTAGA	0	135	0
GAGCGTTTTATTTTCAGTGTACTTGATGTCTAATACAAATT	0	202	1
AGCAGAGCTCTTTTTTGAAGATTCTTCTTTTTTCTTAGGTC	1	10	1
TTCTTCTTTTTTCTTAGGTCATTCTGGGTTTTTTGAAGGTA	1	31	1
ATCCCACGATTCTTTTGTATAGAAAAATTTTATGAAAGCTT	1	130	1
GACTTTTTATTTTTCAAATAAAAACGTTTTTAAAAATATTA	1	185	1
ATTATTATCATAATTAGATACTTATTTGTTTTAATGTCTTA	1	222	1
TTTTAATGTCTTATTTGATTAAAATAACTTTGTTAAAATTT	1	250	1
GCTCTTTGCATACTTTGCTTAGAGCAGTTTTTGGTTCTCAG	3	16	1
CAGTTTTTGGTTCTCAGGGTCGTTTGCCTTTAGGGAGCTTG	3	40	1
CTGATTTTGATTATTAGAAAATAATAGATTTTTTCTGTTTT	3	234	1
TTTTTTCTGTTTTTTAAAGTAAAGTATTTTTTAAAAGACTC	3	262	1
          *  ****   * *     ***
MAP Score: 12.3964

Motif 2
CCTCAAACCGTCGAATTTTCTTTGTCT     	0	5	0
AACAAATACGTTATCGATTCTTAGGGGAAATA	0	151	0
AAATTGTTTATTTTGTATTTTTGGCACATCAT	0	238	1
GAGCTCTTTTTTGAAGATTCTTCTTTTTTCTT	1	14	1
TCTTAGGTCATTCTGGGTTTTTTGAAGGTATC	1	42	1
TTTGAAGGTATCGAGGGTTCTTATTGTCTAGT	1	62	1
ATAGAGGGTATCGAGGTTTTTTCTCTTAGGTA	1	99	1
TCTTAGGTATCCCACGATTCTTTTGTATAGAA	1	122	1
TTTACACTGACTTTTTATTTTTCAAATAAAAA	1	177	1
CTTAGAGCAGTTTTTGGTTCTCAGGGTCGTTT	3	33	1
TCCCCGATGGTCCTTTGTTTTTATCTCTAACA	3	155	0
ATCTCTATTCCTATAGATTTTTGCTGATTTTG	3	211	1
ACAGAAAAAATCTATTATTTTCTAATAATCAA	3	240	0
ATAATAGATTTTTTCTGTTTTTTAAAGTAAAG	3	254	1
          ** * *******
MAP Score: 10.3221

Motif 3
TTATCCTCAAACCGTCGAATTTTCTTTGTCT    	0	6	0
ACGCCTGTAAAGCAGAGTATCCTGATTCAAAGCTT	0	56	0
ACTCTGCTTTACAGGCGTGTCTTTGTGCCTATGGT	0	73	1
TCTCTCTCATAACAGAGTCTCTCAAATCTAATTGT	0	109	1
AACGTGCTCAACAAGAGCGTTTTATTTTCAGTGTA	0	188	1
          AGCAGAGCTCTTTTTTGAAGATTCT	1	0	1
ACCTAAGAAAAAAGAAGAATCTTCAAAAAAGAGCT	1	15	0
TTTTGAAGGTATCGAGGGTTCTTATTGTCTAGTTG	1	61	1
TATAGAGGGTATCGAGGTTTTTTCTCTTAGGTATC	1	98	1
TAAAAATTTTAACAAAGTTATTTTAATCAAATAAG	1	259	0
GATGTTTGGGATCGGAGAGCCTCCTTATATCCCTA	3	82	1
ACAAAGGACCATCGGGGAGACTTGTACTCATAAGA	3	169	1
AGGAATAGAGATAAGTGGCTCTTATGAGTACAAGT	3	188	0
         TAAAAATGAGTCTTTTAAAAAATACT	3	284	0
          * *** *  **** *
MAP Score: 8.97488

Motif 4
TGTCTAATACAAATTGTTTATTTTGTATTTT	0	228	1
CTCTTTTTTGAAGATTCTTCTTTTTTCTTAG	1	17	1
GAAGGTATCGAGGGTTCTTATTGTCTAGTTG	1	65	1
GAGGGTATCGAGGTTTTTTCTCTTAGGTATC	1	102	1
AAGCTTTCATAAAATTTTTCTATACAAAAGA	1	140	0
CTCTTTACACTGACTTTTTATTTTTCAAATA	1	174	1
TATTTTTAAAAACGTTTTTATTTGAAAAATA	1	192	0
TAACTTTGTTAAAATTTTTATACATAAATTT	1	274	1
CTATTCCTATAGATTTTTGCTGATTTTGATT	3	215	1
AGAAAATAATAGATTTTTTCTGTTTTTTAAA	3	249	1
          *** *******
MAP Score: 7.72675

Motif 5
       AGACAAAGAAAATTCGACGGTTTG	0	3	1
ACATCAAGTACACTGAAAATAAAACGCTCTT	0	200	0
ATGTGCCAAAAATACAAAATAAACAATTTGT	0	236	0
CCAGAATGACCTAAGAAAAAAGAAGAATCTT	1	27	0
TGGGATACCTAAGAGAAAAAACCTCGATACC	1	105	0
GATTCTTTTGTATAGAAAAATTTTATGAAAG	1	137	1
AAACGTTTTTATTTGAAAAATAAAAAGTCAG	1	183	0
ATAAGACATTAAAACAAATAAGTATCTAATT	1	233	0
          AATAGAAATTTATGTATAAAA	1	289	0
GAGGGTCTGTTAGAGATAAAAACAAAGGACC	3	148	1
AATAATCAAAATCAGCAAAAATCTATAGGAA	3	218	0
GATTTTGATTATTAGAAAATAATAGATTTTT	3	236	1
TACTTTAAAAAACAGAAAAAATCTATTATTT	3	252	0
          ** ********
MAP Score: 4.98472

Motif 6
TTATCCTCAAACCGTCGAATTTTCTTTGTCT    	0	6	0
CCTAAGAATCGATAACGTATTTGTTAGGAAAACGT	0	158	1
CGTGCTCAACAAGAGCGTTTTATTTTCAGTGTACT	0	190	1
GTCTAATACAAATTGTTTATTTTGTATTTTTGGCA	0	229	1
TCTTTTTTGAAGATTCTTCTTTTTTCTTAGGTCAT	1	18	1
TATAGAGGGTATCGAGGTTTTTTCTCTTAGGTATC	1	98	1
AACTCTTTACACTGACTTTTTATTTTTCAAATAAA	1	172	1
TAATATTTTTAAAAACGTTTTTATTTGAAAAATAA	1	191	0
TATCATAATTAGATACTTATTTGTTTTAATGTCTT	1	227	1
TATTTGTTTTAATGTCTTATTTGATTAAAATAACT	1	244	1
TACTTTGCTTAGAGCAGTTTTTGGTTCTCAGGGTC	3	26	1
AAACAGAAAAAATCTATTATTTTCTAATAATCAAA	3	239	0
TGTTTTTTAAAGTAAAGTATTTTTTAAAAGACTCA	3	269	1
          *    ******** *
MAP Score: 4.38006

Motif 7
CTTTACAGGCGTGTCTTTGTGCCTATGGTCTCTC	0	79	1
TTTGTGCCTATGGTCTCTCTCTCATAACAGAGTC	0	94	1
CTCAACAAGAGCGTTTTATTTTCAGTGTACTTGA	0	194	1
TTATTTTCAGTGTACTTGATGTCTAATACAAATT	0	209	1
ATACAAATTGTTTATTTTGTATTTTTGGCACATC	0	234	1
CTTTTTTGAAGATTCTTCTTTTTTCTTAGGTCAT	1	19	1
AGGTATCGAGGGTTCTTATTGTCTAGTTGTCTAT	1	67	1
AGAGGGTATCGAGGTTTTTTCTCTTAGGTATCCC	1	101	1
TCTTTACACTGACTTTTTATTTTTCAAATAAAAA	1	175	1
AGATACTTATTTGTTTTAATGTCTTATTTGATTA	1	237	1
CGATGGTCCTTTGTTTTTATCTCTAACAGACCCT	3	149	0
GAAAATAATAGATTTTTTCTGTTTTTTAAAGTAA	3	250	1
          * *****  * ***
MAP Score: 3.19491

Motif 8
TGTCTAATACAAATTGTTTATTTTGTATTTTTGGCACATCA	0	228	1
TTGGCACATCATTTAAATTCCTTGTACTTTTGAATCTAAAC	0	258	1
     AGCAGAGCTCTTTTTTGAAGATTCTTCTTTTTTCTT	1	5	1
ATCCCACGATTCTTTTGTATAGAAAAATTTTATGAAAGCTT	1	130	1
TGAAAGCTTGAACTCTTTACACTGACTTTTTATTTTTCAAA	1	162	1
ATTATGATAATAATATTTTTAAAAACGTTTTTATTTGAAAA	1	195	0
TTATTATCATAATTAGATACTTATTTGTTTTAATGTCTTAT	1	223	1
TATTTGATTAAAATAACTTTGTTAAAATTTTTATACATAAA	1	261	1
AGAGCCACTTATCTCTATTCCTATAGATTTTTGCTGATTTT	3	201	1
TATTAGAAAATAATAGATTTTTTCTGTTTTTTAAAGTAAAG	3	245	1
          *  *   ***  *    ****
MAP Score: 1.76411