AlignACE 3.0 10/20/99
AlignACE2 -i CY/CY_fusions013_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944246575
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	hypothetical	167	hypothetical protein
#1	mannose-1-phosphate	165	mannose-1-phosphate guanyltransferase
#2	sucD	104	succinyl-CoA synthetase
#3	hypothetical	171	hypothetical protein
#4	regulatory	300	regulatory components of sensory transduction system
#5	hypothetical	300	hypothetical protein
#6	hypothetical	171	hypothetical protein
#7	rfbA	157	glucose-1-phosphate thymidylyltransferase

Motif 1
TAACTGCTCCGGGAAATTTCAGGTAAATCA	0	111	0
AATTGTGTGAGGAAAATTTTCAG       	0	154	1
TTGAGTTTGAGGAAAATTGTTG        	1	153	1
          GGGACATTTTGCTCTGGTTG	2	0	1
        GGGGGGATTATTAAAGGAAAAC	2	92	0
  GACTCCAAGGGCAATAGTACTGAAATCG	3	8	1
GATTAAGGTGGGGGCATATTGTGGTGGTGC	3	70	0
AAGAGATTACGGAAAATTTAAGGAAAATAA	4	37	0
TTTTTTGTTAGGGGAGTTTTCTGGGCGGCA	4	195	0
         AGGGCCATATTTAGCTAAATA	5	1	1
ACCATCATTAGGGACTTTTATTTATTAATT	5	30	1
GGCTATGTCTGGGTATTTTTACCGAGATAA	5	89	1
TCTTGATTTTGGGACAATTTATCTCGGTAA	5	107	0
GCAAGACTTGGGGAAATTTTTAAAATAGTT	5	164	0
GCAGTTTCAAGGGACAATTCA         	5	289	1
AGAAATTGTTGGGGAGTATTTTACAAACCT	6	55	1
GTAGAAACTAGGGAAATTGAAGCAAAATAG	6	139	0
AAGTTGAGATGGGGCATAGAGATTTTTGAT	7	73	1
          **********
MAP Score: 19.161

Motif 2
GACGATTTGTAAAAATCCGCCCAATTTTTAAATT	0	26	0
AAATTTCAGGTAAATCACGCCCCACTGGATTGCC	0	94	0
GTGATTTACCTGAAATTTCCCGGAGCAGTTATCC	0	110	1
       CTGAAAATTTTCCTCACACAATTCTTC	0	150	0
GCGGGAAAGCAGAATCTATCTCCATCATCTTTGC	1	11	0
        CAACAATTTTCCTCAAACTCAATCAC	1	149	0
CAGTTTTCCTTTAATAATCCCCCC          	2	90	1
CAGCACCACCACAATATGCCCCCACCTTAATCCT	3	68	1
CTTATTTTCCTTAAATTTTCCGTAATCTCTTCTT	4	36	1
TAATCTCTTCTTAAAGTTGCTCCCCTACTCCCAA	4	58	1
TCTGCCGCCCAGAAAACTCCCCTAACAAAAAAAT	4	193	1
GACATAGCCATTAAAATCGCTCAATTTTTCTTCT	5	64	0
TTTATCTCGGTAAAAATACCCAGACATAGCCATT	5	86	0
TTTTACCGAGATAAATTGTCCCAAAATCAAGAAT	5	105	1
AAACTATTTTAAAAATTTCCCCAAGTCTTGCTCC	5	163	1
AATTGTCCCTTGAAACTGCCTCCAGATTAACAGA	5	274	0
CTAGGTTTGTAAAATACTCCCCAACAATTTCTGA	6	53	0
          * *** * **** *
MAP Score: 17.872

Motif 3
TGGGGCGTGATTTACCTGAAATTTCCCGGAGCAGTTA	0	104	1
   CTGAAAATTTTCCTCACACAATTCTTCCTCTCAG	0	143	0
ATAGATTCTGCTTTCCCGCCAGCGGTCACCATGGGGT	1	26	1
    CAACAATTTTCCTCAAACTCAATCACACAAGTT	1	142	0
CAAGCCACAGTTTTCCTTTAATAATCCCCCC      	2	83	1
GTTTTTTGGTTTTTCCTAGCAGCACCACCACAATATG	3	49	1
ATTTTTAAGTTATTGCTCCACTCCCTCCAGTTGATGG	3	107	1
TTAAATCTTATTTTCCTTAAATTTTCCGTAATCTCTT	4	30	1
CCTCATGTCTCTTTGCTCACCATGATTTTTTTGTTAG	4	214	0
TTCTCCATTATTTTCCTACCTCATGTCTCTTTGCTCA	4	232	0
AATGATGGTATTTAGCTAAATATGGCCCT        	5	2	0
          TTTTCCTTTACGCTGTTGTTTTGTCTG	6	0	1
GGTTTGGCTATTTTGCTTCAATTTCCCTAGTTTCTAC	6	132	1
CTAACCGACCCATTGCTCCCTTGCCCT          	7	0	0
TGGTGGTGGCTTTTGCCTTCCCTAACCGACCCATTGC	7	21	0
          *******  *     **
MAP Score: 12.0981

Motif 4
CAGAATTTAAAAATTGGGCGGATTTTTACAA	0	23	1
CTGAGAGGAAGAATTGTGTGAGGAAAATTTT	0	143	1
GAGTTATGCCAACTTGTGTGATTGAGTTTGA	1	132	1
TTTTGCCATCAACTGGAGGGAGTGGAGCAAT	3	118	0
GTTGATGGCAAAATTGCTTGCCGGTATTTGT	3	136	1
TACTCCCAAAAACTTGATTCAAGTCCTTTTT	4	83	1
TTAAGAAGAAAAATTGAGCGATTTTAATGGC	5	61	1
TTACCGAGATAAATTGTCCCAAAATCAAGAA	5	107	1
CCTAGAGTCTAAATTGAGTGAACTAAGAATC	5	243	1
AATGGGTCAGAAATTGTTGGGGAGTATTTTA	6	47	1
GCCCCATCTCAACTTGCCTGATATGTTTATT	7	57	0
ATCTGCCCGTAAATTGACTGATTTCGTGTCA	7	105	0
          ****** ****
MAP Score: 10.1251

Motif 5
CTCAGTTGTGCCCTCAAGTGAGCAGCAGTAATGAAG	4	138	0
TTGCTCCACTCCCTCCAGTTGATGGCAAAATTGCTT	3	119	1
ATTCTGCTTTCCCGCCAGCGGTCACCATGGGGTTAG	1	30	1
CCATTAAAATCGCTCAATTTTTCTTCTTAAAAATTA	5	55	0
GTTAGTTACTCCTCCAAGCTTTCAGCTATGCTTATT	1	61	1
CAAACTCAATCACACAAGTTGGCATAACTCACCCGC	1	126	0
TAAAATACTCCCCAACAATTTCTGACCCATTCACCG	6	42	0
TTAAAAATTTCCCCAAGTCTTGCTCCCTACCTAGAT	5	171	1
AAATTTTCCTCACACAATTCTTCCTCTCAGGATAAC	0	137	0
TAAGCATCTGCCCGTAAATTGACTGATTTCGTGTCA	7	105	0
GCGTGATTTACCTGAAATTTCCCGGAGCAGTTATCC	0	108	1
ATCTTATTTTCCTTAAATTTTCCGTAATCTCTTCTT	4	34	1
GCATAACTCACCCGCCAGTCTATCAAGATTCTTCTC	1	105	0
CTCCCCTACTCCCAAAAACTTGATTCAAGTCCTTTT	4	77	1
CTTGAAACTGCCTCCAGATTAACAGAGATTCTTAGT	5	264	0
ATTCTTAGTTCACTCAATTTAGACTCTAGGTATAAA	5	237	0
AGGTAAATCACGCCCCACTGGATTGCCTCAGGGGTT	0	85	0
TTGTAAAAATCCGCCCAATTTTTAAATTCTGATTCC	0	18	0
          *** *** **  *  *
MAP Score: 6.11781

Motif 6
TATCCTGAGAGGAAGAATTGTGTGAGGAAAATTT	0	139	1
TCCAGTTGATGGCAAAATTGCTTGCCGGTATTTG	3	132	1
AAAAGGACTTGAATCAAGTTTTTGGGAGTAGGGG	4	79	0
CTCACTTGAGGGCACAACTGAGTTTGGCGATCGC	4	152	1
TATAATGGTAGTCAAAACTATTTTAAAAATTTCC	5	149	1
TATACCTAGAGTCTAAATTGAGTGAACTAAGAAT	5	239	1
CGGTGAATGGGTCAGAAATTGTTGGGGAGTATTT	6	42	1
AACCTAGTTTGGATAAAATTGTTGAGCTTATAAG	6	80	1
          * ** ** ** ***
MAP Score: 1.20523

Motif 7
GCGGACGTTCAACCCCTGAGGCAATCCAGTGGGGCGTGATTTA	0	75	1
CCCGGAGCAGTTATCCTGAGAGGAAGAATTGTGTGAGGAAAAT	0	128	1
AGATTCTGCTTTCCCGCCAGCGGTCACCATGGGGTTAGTTACT	1	28	1
GGACTGGTTGACCCCGATAGCTGCGGAGTAGGGCATCAAGCCA	2	47	1
GTCTCTTTGCTCACCATGATTTTTTTGTTAGGGGAGTTTTCTG	4	202	0
AGGGCCATATTTAGCTAAATACCATCATTAGGGACTTTTATTT	5	10	1
AAGCGTTTTTATACCTAGAGTCTAAATTGAGTGAACTAAGAAT	5	230	1
GAATCTCTGTTAATCTGGAGGCAGTTTCAAGGGACAATTCA  	5	269	1
CGCTGTTGTTTTGTCTGAAGTTCGGTGAATGGGTCAGAAATTG	6	20	1
          * ***   **         ****
MAP Score: 0.575002