AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_fusions004_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241529
 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
AAAGTTTGCTTTCTTTTTTAAAAAAATCTTTGCTA	0	57	0
CAGATTAACAACCTTTTTATACAGATAAAAGTTTG	0	84	0
GTTAATCTGTTTCTTTTTCAAAAAAAGTTTGTGTA	0	110	1
AGTAAAATACTTCTGTTTGATGGGAGGGGGGGGGG	0	192	0
AAAGGGAGGCAACTTTTGATACCCAACTATACTTA	0	246	0
AGGCCTGTTTTGCTTTTTGTAAAAATACTTTTGCA	1	155	1
TTTGTAAAAATACTTTTGCAAGGAAGTGAGAGTAG	1	170	1
ATCACCAGCCTCCTTCTAAAGGGAAGCCTTTCCGC	1	224	0
AAACTGATTCTTCTTTTAATCACCAGCCTCCTTCT	1	242	0
TCTCTATTATTTCTTTTATTTGACACACCTTACTC	2	11	1
TTAGCTTAATAGCTTTTAGAAGACAATACGTTTGC	2	103	0
ATTTTTCTTAAGCTTCTAGAGCAAACACACTTGAA	2	261	1
          TTCTTTTGTTTACGATTTTTCTGC 	3	0	1
          * *****  * ** *
MAP Score: 11.5942

Motif 3
GAGATAGACCCTCTTTACACAAACTTTTTTTG	0	128	0
AGTTTGCTTTCTTTTTTAAAAAAATCTTTGCT	0	58	0
GCCTGTTTTGCTTTTTGTAAAAATACTTTTGC	1	157	1
TAATCTGTTTCTTTTTCAAAAAAAGTTTGTGT	0	112	1
CCTACTCCCTCTCTTTACACAGCAAACGTATT	2	82	1
GATTAACAACCTTTTTATACAGATAAAAGTTT	0	85	0
AATCACCAGCCTCCTTCTAAAGGGAAGCCTTT	1	228	0
AATTCAAAGTCTTATTGAAAAACGTAATGAGC	1	50	1
CTACTCTCACTTCCTTGCAAAAGTATTTTTAC	1	173	0
GCCCGGGCATCATATTGGACAATTGTAGTAAT	2	158	0
CTAAGTACGGCTTATTAAAAGGGAGGCAACTT	0	266	0
          ******  ****
MAP Score: 10.5601

Motif 4
CCATGCTCTAGGGGTAGGGGCATCCTGAAT	1	118	0
TTGATGGGAGGGGGGGGGGGGAGAATAAAA	0	181	0
GTAAAGAGAGGGAGTAGGGGTGAGGATGCG	2	70	0
TTTTTTATTCGTAGTAGGGGAACAGGCTCT	4	11	0
GTAGAGAACAGGGATATGGGCGGAAAGGCT	1	205	1
          **********
MAP Score: 8.00488

Motif 5
ATGGGAGGGGGGGGGGGGAGAATAAAAATT	0	178	0
TACTTCTGTTTGATGGGAGGGGGGGGGGGG	0	190	0
ACGGCTTATTAAAAGGGAGGCAACTTTTGA	0	262	0
CCCCATGCTCTAGGGGTAGGGGCATCCTGA	1	120	0
TACCCCTAGAGCATGGGGAGGTTAGGCCTG	1	132	1
TGCAAGGAAGTGAGAGTAGGTAGAGAACAG	1	186	1
AGCCTCCTTCTAAAGGGAAGCCTTTCCGCC	1	223	0
GGCTTCCCTTTAGAAGGAGGCTGGTGATTA	1	231	1
ATGGATAAGCGGAGAGTAAGGTGTGTCAAA	2	29	0
AGAGAGGGAGTAGGGGTGAGGATGCGGCGT	2	66	0
TGCTGTGTAAAGAGAGGGAGTAGGGGTGAG	2	76	0
AATTTTTTATTCGTAGTAGGGGAACAGGCT	4	13	0
          **********
MAP Score: 2.81067

Motif 6
TGAATTCAAAGTCTTATTGAAAAACGTAATGAG	1	48	1
GTCTAGCCTAGACTGATAGCAAAAAACGAGGTC	2	192	1
ATGAGCTTGTGCCTAACGGAAAATCATGATAGC	1	76	1
ATCTAGTATTGCGTGATCGAAAAAATTTTTTAT	4	33	0
TTTTTCAGTTGCTTAATGGCAAACTGATTCTTC	1	264	0
GTATAGCAAAGATTTTTTTAAAAAAGAAAGCAA	0	54	1
GGCCTGTTTTGCTTTTTGTAAAAATACTTTTGC	1	156	1
TGTAAAGAGGGTCTATCTCCAAAAGATAGGAAG	0	141	1
GTTAATCTGTTTCTTTTTCAAAAAAAGTTTGTG	0	110	1
AGCAAACGTATTGTCTTCTAAAAGCTATTAAGC	2	102	1
AAGATTCTCGGAGGTATAGCAAAGATTTTTTTA	0	41	1
AGAGTAAGGTGTGTCAAATAAAAGAAATAATAG	2	14	0
          * ** ** *****
MAP Score: 2.57073