AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_fusions004_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241513
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	CT260	300	hypothetical protein
#1	CT538	300	hypothetical protein
#2	uhpC	300	Hexosphosphate Transport
#3	uvrC	24	Excinuclease ABC, Subunit C
#4	mutS	62	DNA Mismatch Repair

Motif 1
AGATTTTTTTAAAAAAGAAAGCAAACTTTT	0	63	1
TTTTATACAGATAAAAGTTTGCTTTCTTTT	0	75	0
AACTTTTTTTGAAAAAGAAACAGATTAACA	0	109	0
TTCTTTTTCAAAAAAAGTTTGTGTAAAGAG	0	120	1
CAAAAGATAGGAAGAAGAAATTTTTATTCT	0	160	1
CTCCCATCAAACAGAAGTATTTTACTCTGC	0	201	1
CTTGCTCGACATAGAAGTTTTTCATTTGAA	1	22	1
AGTCTTATTGAAAAACGTAATGAGCTTGTG	1	57	1
TCACTTCCTTGCAAAAGTATTTTTACAAAA	1	169	0
CTGGTGATTAAAAGAAGAATCAGTTTGCCA	1	251	1
TAAGCAACTGAAAAAAGTAAGGATAAGT  	1	282	1
GGTGTGTCAAATAAAAGAAATAATAGAGAG	2	10	0
TCTTTACACAGCAAACGTATTGTCTTCTAA	2	93	1
AAGCTAAATGAAAGGAGTATTGACGACATT	2	131	1
GCATACTGAGACGAAAGTATCAGCTTCTAA	2	225	0
          **********
MAP Score: 11.6831

Motif 2
ATTTTTTTAAAAAAGAAAGCAAACTTTTATC	0	65	1
ACTTTTTTTGAAAAAGAAACAGATTAACAAC	0	107	0
GTCTATCTCCAAAAGATAGGAAGAAGAAATT	0	151	1
CCCTCCCATCAAACAGAAGTATTTTACTCTG	0	199	1
CGGCTTATTAAAAGGGAGGCAACTTTTGATA	0	260	0
GCCTCCTTCTAAAGGGAAGCCTTTCCGCCCA	1	221	0
GGCTGGTGATTAAAAGAAGAATCAGTTTGCC	1	249	1
AGCAACTGAAAAAAGTAAGGATAAGT     	1	284	1
AAGGTGTGTCAAATAAAAGAAATAATAGAGA	2	11	0
TTTGCTGTGTAAAGAGAGGGAGTAGGGGTGA	2	77	0
CTATTAAGCTAAATGAAAGGAGTATTGACGA	2	126	1
GAAAAATCGTAAACAAAAGAA          	3	0	0
          *** *******
MAP Score: 10.5325

Motif 3
ATTAACAACCTTTTTATACAGATAAAAGTTTG	0	84	0
ACTGATTCTTCTTTTAATCACCAGCCTCCTTC	1	243	0
TGCAAAAGTATTTTTACAAAAAGCAAAACAGG	1	158	0
TTTGCTTTCTTTTTTAAAAAAATCTTTGCTAT	0	56	0
CTACTCCCTCTCTTTACACAGCAAACGTATTG	2	83	1
AGTTGCCTCCCTTTTAATAAGCCGTACTTAGA	0	267	1
AGCTTAATAGCTTTTAGAAGACAATACGTTTG	2	104	0
AGATAGACCCTCTTTACACAAACTTTTTTTGA	0	127	0
TCGAAAAAATTTTTTATTCGTAGTAGGGGAAC	4	18	0
GAAAGGCTTCCCTTTAGAAGGAGGCTGGTGAT	1	227	1
AATCTGTTTCTTTTTCAAAAAAAGTTTGTGTA	0	113	1
GAAGAAGAAATTTTTATTCTCCCCCCCCCCCC	0	170	1
TGCATTTGTATTTTTCTTAAGCTTCTAGAGCA	2	252	1
TCTATTATTTCTTTTATTTGACACACCTTACT	2	13	1
          ****** *** *
MAP Score: 7.65615

Motif 4
ATAGCAAAGATTTTTTTAAAAAAGAAAGCAAACT	0	56	1
CAAACTTTTATCTGTATAAAAAGGTTGTTAATCT	0	84	1
ACAAACTTTTTTTGAAAAAGAAACAGATTAACAA	0	108	0
TCAAAAAAAGTTTGTGTAAAGAGGGTCTATCTCC	0	127	1
AAAATACTTCTGTTTGATGGGAGGGGGGGGGGGG	0	190	0
AGTATTTTACTCTGCCGAAAAAACAACACTTAAG	0	216	1
AAGTACGGCTTATTAAAAGGGAGGCAACTTTTGA	0	262	0
GAATTCAAAGTCTTATTGAAAAACGTAATGAGCT	1	49	1
TGCAAAAGTATTTTTACAAAAAGCAAAACAGGCC	1	156	0
TGTAAAAATACTTTTGCAAGGAAGTGAGAGTAGG	1	172	1
AGAACAGGGATATGGGCGGAAAGGCTTCCCTTTA	1	209	1
GAAAGGCTTCCCTTTAGAAGGAGGCTGGTGATTA	1	227	1
ATACGTTTGCTGTGTAAAGAGAGGGAGTAGGGGT	2	79	0
GCAAACGTATTGTCTTCTAAAAGCTATTAAGCTA	2	103	1
TTCAAGTGTGTTTGCTCTAGAAGCTTAAGAAAAA	2	262	0
          * **   *******
MAP Score: 6.54654

Motif 5
ATTCAGGATGCCCCTACCCCTAGAGCATGG	1	118	1
CGCATCCTCACCCCTACTCCCTCTCTTTAC	2	70	1
TTTATTCTCCCCCCCCCCCCTCCCATCAAA	0	182	1
AGAGCCTGTTCCCCTACTACGAATAAAAAA	4	11	1
AGCCTTTCCGCCCATATCCCTGTTCTCTAC	1	205	0
ATCCACAATACGCCGCATCCTCACCCCTAC	2	57	1
TCTTTTAATCACCAGCCTCCTTCTAAAGGG	1	236	0
          **********
MAP Score: 6.08732

Motif 6
CTTTCTTTTTTAAAAAAATCTTTGCTATACCTCCG	0	49	0
ACTTTTATCTGTATAAAAAGGTTGTTAATCTGTTT	0	87	1
TGTTTCTTTTTCAAAAAAAGTTTGTGTAAAGAGGG	0	117	1
CAAAAGATAGGAAGAAGAAATTTTTATTCTCCCCC	0	160	1
TTTCGGCAGAGTAAAATACTTCTGTTTGATGGGAG	0	201	0
GAATTCAAATGAAAAACTTCTATGTCGAGCAAGAA	1	20	0
TTGCTTTTTGTAAAAATACTTTTGCAAGGAAGTGA	1	164	1
GTGATTAAAAGAAGAATCAGTTTGCCATTAAGCAA	1	254	1
AGCTTTTAGAAGACAATACGTTTGCTGTGTAAAGA	2	93	0
AGAAGCTTAAGAAAAATACAAATGCATACTGAGAC	2	243	0
CCCCTACTACGAATAAAAAATTTTTTCGATCACGC	4	21	1
          * * ** *  *****
MAP Score: 5.84149

Motif 7
TGTAAAGAGAGGGAGTAGGGGTGAGGATGC	2	71	0
CCCATGCTCTAGGGGTAGGGGCATCCTGAA	1	119	0
GCTTCCCTTTAGAAGGAGGCTGGTGATTAA	1	232	1
TGATGGGAGGGGGGGGGGGGAGAATAAAAA	0	180	0
CGGCTTATTAAAAGGGAGGCAACTTTTGAT	0	261	0
TGGATAAGCGGAGAGTAAGGTGTGTCAAAT	2	28	0
CCCCTAGAGCATGGGGAGGTTAGGCCTGTT	1	134	1
GGGAGTAGGGGTGAGGATGCGGCGTATTGT	2	61	0
GCAAGGAAGTGAGAGTAGGTAGAGAACAGG	1	187	1
TTCGTAGTAGGGGAACAGGCTCTT      	4	4	0
GCCTCCTTCTAAAGGGAAGCCTTTCCGCCC	1	222	0
AAAAGTTTGTGTAAAGAGGGTCTATCTCCA	0	132	1
GGTAGAGAACAGGGATATGGGCGGAAAGGC	1	204	1
TCCAAAAGATAGGAAGAAGAAATTTTTATT	0	158	1
AGCAACTGAAAAAAGTAAGGATAAGT    	1	284	1
CGTATTGTGGATGGATAAGCGGAGAGTAAG	2	39	0
          **********
MAP Score: 5.0198

Motif 8
GTTTGATGGGAGGGGGGGGGGGGAGAATAAAAATTTC	0	176	0
CCCTACCCCTAGAGCATGGGGAGGTTAGGCCTGTTTT	1	129	1
GGTAGAGAACAGGGATATGGGCGGAAAGGCTTCCCTT	1	204	1
TGTAAAGAGAGGGAGTAGGGGTGAGGATGCGGCGTAT	2	64	0
GGATAAGCGGAGAGTAAGGTGTGTCAAATAAAAGAAA	2	20	0
CCCATGCTCTAGGGGTAGGGGCATCCTGAATCGACTA	1	112	0
CCCTTTAGAAGGAGGCTGGTGATTAAAAGAAGAATCA	1	236	1
GTGAGGATGCGGCGTATTGTGGATGGATAAGCGGAGA	2	44	0
          ****   **** *   *
MAP Score: 4.72832

Motif 9
CTTAAGATTCTCGGAGGTATAGCAAAGATTTTTTTAAAAAA	0	38	1
TGATGGGAGGGGGGGGGGGGAGAATAAAAATTTCTTCTTCC	0	169	0
CCTACCCCTAGAGCATGGGGAGGTTAGGCCTGTTTTGCTTT	1	130	1
AAGGAAGTGAGAGTAGGTAGAGAACAGGGATATGGGCGGAA	1	189	1
CCTTTAGAAGGAGGCTGGTGATTAAAAGAAGAATCAGTTTG	1	237	1
TATTGTGGATGGATAAGCGGAGAGTAAGGTGTGTCAAATAA	2	26	0
TGTGTAAAGAGAGGGAGTAGGGGTGAGGATGCGGCGTATTG	2	62	0
TATGATGCCCGGGCTGGTCTAGCCTAGACTGATAGCAAAAA	2	176	1
          * *   *  ***   ***  *
MAP Score: 4.29014

Motif 10
TTATTCTCCCCCCCCCCCCTCCCATCAAACAGA	0	183	1
GGAAGCCTTTCCGCCCATATCCCTGTTCTCTAC	1	205	0
ACACCTTACTCTCCGCTTATCCATCCACAATAC	2	35	1
GCCGCATCCTCACCCCTACTCCCTCTCTTTACA	2	68	1
          * ****  *****
MAP Score: 1.72244

Motif 11
CTCGGAGGTATAGCAAAGATTTTTTTAAAAAAGAA	0	47	1
TTAAAAAAGAAAGCAAACTTTTATCTGTATAAAAA	0	71	1
AAAGAAACAGATTAACAACCTTTTTATACAGATAA	0	91	0
GACCCTCTTTACACAAACTTTTTTTGAAAAAGAAA	0	119	0
GGGGGGGGAGAATAAAAATTTCTTCTTCCTATCTT	0	163	0
CCCCCTCCCATCAAACAGAAGTATTTTACTCTGCC	0	197	1
ATAGTTGGGTATCAAAAGTTGCCTCCCTTTTAATA	0	251	1
TTTCATTTGAATTCAAAGTCTTATTGAAAAACGTA	1	41	1
ATTTTCCGTTAGGCACAAGCTCATTACGTTTTTCA	1	65	0
CTCACTTCCTTGCAAAAGTATTTTTACAAAAAGCA	1	165	0
CTCTTTACACAGCAAACGTATTGTCTTCTAAAAGC	2	92	1
TATTAAGCTAAATGAAAGGAGTATTGACGACATTA	2	127	1
GACTGATAGCAAAAAACGAGGTCTTAGAAGCTGAT	2	202	1
CCCTACTACGAATAAAAAATTTTTTCGATCACGCA	4	22	1
          *  *****  ** **
MAP Score: 0.673809